Gromos related commands (GROMOS)

Introduction.

The main menu option GROMOS brings you to the menu from which you can run several GROMOS related commands, ranging from checking the energy of a structure to starting a full scaleMD run. This WHATIF GROMOS interface is maintained by Daan van Aalten, which, if you have specific questions, you can mail at bmb5dva@biovax.leeds.ac.uk

If you are a GROMOS lisence holder, you can get our versions of the GROMOS source code too. Although they are normally compatible with the official versions, we sometimes made some clones that give a slightly altered result for some special purposes. These altered versions will also ONLY be redistributed to official GROMOS lisence holders.

Be aware that there are several other places where commands can be given that are somewhat related to the usage of GROMOS.

The menu ANATRA (see chapter on moleculat dynamics trajectories) deals with all kinds of options to evaluate molecular dynamics trajectories.

Setting up GROMOS for use with WHAT IF:

To use GROMOS, WHAT IF requires the following files in the directory ..../whatif/wregro directory:

Executables		Parameter files
PROIONL.EXE		IFP37D4.DAT            
PROMDL.EXE		RT37D.DAT
PROMDL.EXE		IFP37C4.DAT           
PROMMTL.EXE		RT37C.DAT
PROEML.EXE		RT37DNEW.DAT          
PROGCHL.EXE		SPC216.DAT            
PROGMTL.EXE		SSS.RESLIB
PROGWHL.EXE           
PROSDL.EXE        
PROBOXL.EXE                        
PROEMAL.EXE

These files are normally NOT distributed by us, unless you are a lisenced GROMOS user, and explicitly requested the GROMOS distribution files to be distributed with WHAT IF.

Automatic options (READ THIS IF YOU WANT TO USE EM/MD WITHOUT GETTING INTO DETAILS) (FASTXX)

If you just want to run a short simple MD run, e.g. to refine a mutant, please read this and skip the rest of this chapter. Any other experienced GROMOS user may also be interested in reading this section, because it may considerably increase the speed at which you can startup your MD runs. Simply read in your PDB file and type GROMOS to go into the GROMOS menu. Then type PARAMS to get into the GROMOS parameters menu. The following flags you may need to change to suit your needs:

STEPS	Number of EM steps (default = 5 ps)
HTSTEP	Length of your initial MD run (deafult = 5 ps)
MDSTEP	Length of your continuation MD run (default = 50 ps)

Then go back to the GROMOS menu by typing END. There are now three options: FASTEM, FASTHT, FASTMD. FASTEM does everything to prepare ALL the molecules you have in the soup for use in GROMOS and then runs an EM run. The resulting GROMOS coordinate file is called WRE-EMGRO(10).DAT. FASTHT does the same as FASTEM, but performs a short (see HTSTEP) MD initilisation run in addition. The atomic trajectories are stored in WRETRACRD(10).DAT1, the final coordinates in WRE-MDGRO(10).DATxx where xx is the value of the HTSTEP parameter. FASTMD does the sam as FASTHT, but performs a long continuation MD run (see MDSTEP) in addition. This MD run is performed in the background, you quit from WHAT IF when you get the WHAT IF> prompt back. Trajectory coordinates (WRETRACRD(10).DATxx) and GROMOS coordinate files (WRE-MDGRO(10).DATxx) are created every picosecond.

Project number (PROJEC)

WHAT IF gives all files that it feeds GROMOS always well defined names. If you want for example multiple energy minimization runs (e.g. seven mutations in the same molecule) a lot of difficulties arise in file nomenclature. Therefore the PROJECT number was introduced. As long as you use a different project number for every molecule or mutant you work on, WHAT IF will not get confused. Project numbers may range from 0 till 89. To the project number 10 is added, and the number that is thus obtained (ranging from 10 till 99) is put in the file name just before the period. So the file WREINPEM.DAT does not exist, but the file WREINPEMxx.DAT does, in which xx are two digits. In principle, the other method to solve the 'confusion' problem is to use multiple directories. In the near future, the project number in all the file names will disappear.

Making GROMOS files for small molecules

Introduction

GROMOS was set up with proteins, nucleic acids and sugars in mind. It is therefore very difficult to make topology files for small molecules (drugs). The program DAVADRUG was constructed to overcome this difficulty. If you perform the WREGRO command (see below) to make everything ready for EM and MD, DAVADRUG is automatically executed to make an accurate topology for drugs not known by GROMOS which you want to simulate.

Gromos preprocessor for small molecules (DAVADRUG)

During execution of the WREGRO command (see below) you will be prompted for the number of a drug molecule. DAVADRUG is executed, reads in the PDB coordinates for the small drug and uses that as the sole input for the construction of the drug topology. On the basis of bond-lengths/angles, and a connection matrix, it determines the SP hybridisation and atom types. You are then confronted with this initial data via a text editor and you can make changes as you please. After you quit from the editor, DAVADRUG starts to determine the GROMOS atom types and adds polar protons. You can add/delete protons interactively. Then DAVADRUG it calculates all angles, improper dihedrals and dihedrals and determines the GROMOS types. The drug topology is added as a building block in the RT37X.DAT file, and you are ready to simulate.

Energy per atom (GETETM)

WHAT IF has the possibility to use a special GROMOS derived energy analyzer to calculate the GROMOS energy per atom. This is not a perfect option, but sometimes it can be illustrative, or indicative for errors in a molecule.

In principle you can get these energy terms by running WREGRO followed by GETETM. If you did run WRUNEM prior to the GETETM option then WHAT IF will automatically take the energy minimized structure rather than the starting configuration.

WHAT IF uses the GROMOS derived program ANALYSE to create a file called WHAT IF.ANA. This file holds the 9 GROMOS energy terms for each atom. Internally these nine terms will be added to form the tenth (total energy) term.

If you run GETETM in a different session from WREGRO, you will be prompted for the residue range that was given to WREGRO earlier. At present it is unclear what will happen if you use WREGRO for more than one protein molecule.

If you want to feed other data to WHAT IF, you can provide a file called WHAT IF.ANA, with the same format as the real one, and answer WHAT IF's question `do you want to use the existing energy terms file` with YES.

Graphical energy output (ETPLOT)

The command ETPLOT in the GRATWO menu (use %ETPLOT from the GROMOS menu ...) plots the energy per atom averaged per residue as function of the residue number.

Gromos pre-processor

Introduction

WHAT IF allows you to do all kinds of GROMOS related operations in a somewhat more user friendly way. The main principle is that as much as possible of all the files needed for what you want is automatically generated. GROMOS facilitates too many options to be covered all by WHAT IF. Nevertheless, you will certainly save many weeks of work thanks to these options. And simple things like energy minimization on a single protein needs no user interaction with GROMOS any more.

Creating topology file (WREGRO)

WHAT IF has a GROMOS preprosessor. The first step is the command WREGRO WREGRO at present allows only for the creation of topology files for single stretches of protein, and the possibility to merge protein topology files, small molecules are allowed as long as there are standard building blocks available. It is also possible to setup EM/MD runs in water.

The command WREGRO will cause WHAT IF to prompt you for a residue range and a pH value. It will then automatically correct for all errors that GROMOS has in its nomenclature, it will automatically take care of all CYS-CYS bridges, and it will determine for all protons whether they are present or absent at the present pH. Subsequently, it will check the hydrogen bonding potentials of all histidines in the range. The possible donor/acceptorship of the histidines NE2/ND1 atoms will be displayed and when there are no contradictions/other difficulties, WHAT IF will automatically make a choice for you. If WHAT IF cannot find a solution, you will be prompted to make a choice between a histidine protonated at ND1 or NE2. It is recommended to check the histidine hydrogen bonds on the screen after WREGRO. After this, several GROMOS programs are executed, ending up with all files necessary to start EM/MD. The GROMOS job/parameter files are generated and presented for editing depending on the setting of the LEVUSE paramater. If LEVUSE > 0, the GROMOS input files are presented to the programs GET???.EXE in the whatif usegro directory, where ??? can be GMT, GCH, GWH, BOX, ION, -EM, or -MD. These programs (written by D.M.F. van Aalten, 10-'93) convert the parameter files to a human readable format. These files are then pulled up in your favourite editor (defined in dbdata/CCONFI.FIG). All the parameters are listed together with their meaning as described in the GROMOS manuals. You can edit the parameters if you want and after you saved the files and quit from your editor, the program PUT???.EXE convert the file you edited back to GROMOS parameter files. Depending on the setting of LEVUSE, the files WREJOB???.COM and WREINP???.DAT (the job and parameter file respectively) will be subsequently pulled up in your editor for editing. If you are not an experienced user, do not edit these files.

WHAT IF will generate the PROGMT job file called WREJOBGMT.COM, the input parameters are stored in WREINPGMT.DAT. PROGMTL.EXE will then be executed interactively. The resulting file WREMTD.BIN will contain the binary GROMOS topology of your system.

Thereafter the GROMOS coordinate file will be written. The 'corrections' needed for GROMOS (ILE CD1 -> ILE CD; VAL CG1 and CG2 swapped; LEU CG1 and CG2 swapped) will be performed. The N- and C-terminus will be modified to NH3 and COO respectively

At this stage, if there are drugs in the selected range, WHAT IF will ask you some questions on how to incorporate them in the topology file. You can add any drug you want if it is described in the RT37D.DAT files with the only limitation that you should take care of the fact that the atom sequence of the drug in the RT37D.DAT file and the soup (= coordinate file you read in) is identical. If the drug is not in the RT37D.DAT file, WHAT IF will automatically call PRODRG unless you already have a drug topology file which is merged to the main protein topology file later. Also, if USEWAT > 0, WHAT IF will aks you for the range of crystallographic water molecules you want to incorporate in the EM/MD run.

Then, WHAT IF will generate the job file called WREJOBGCH.COM and the parameter file WREINPGCH.DAT needed to run PROGCH. Since hydrogen atoms are not generally listed in PDB files, GROMOS adds them to the coordinate file using PROGCH. PROGCHL.EXE is also run interactively.

THE FOLLOWING WILL ONLY HAPPEN IF THE PARAMETER USEWAT > 0

If you also requested to use the waters present in the soup in your EM/MD run, WHAT IF will create a job file called WREJOBGWH.COM and the parameter file WREINPGWH.DAT needed to run PROGWH. Hydrogen atoms of water molecules are also not stores in PDB files (and the soup), so PROGWH is used to add H-atoms to the water oxygens. PROGWH.EXE is run interactively.

THE FOLLOWING WILL ONLY HAPPEN IF THE PARAMETER USEWAT > 1

If you requested periodic boundary conditions (fill a large box with your protein in it with water), WHAT IF creates the job file WREJOBBOX.COM and the parameter file WREINPBOX.DAT for PROBOX. PROBOXL.EXE is run interactively and the number of generated water molecules plus the dimensions of your box will be shown upon termination.

THE FOLLOWING WILL ONLY HAPPEN IF THE TOTAL CHARGE OF YOUR SYSTEM IS NOT ZERO

Immediately after your topology was built (see above), WHAT IF calculates the total charge of your system. If this is not equal to zero, WHAT IF will create a job file WREJOBION.COM and a parameter file WREINPION.DAT

Because you added ions to your system, they also have to be included in the topology, so the job file WREJOBGM2.COM and the parameter file WREINPGM2.DAT. Again, PROGMTL.EXE is run.

At the end of the WREGRO run, you will find a couple of files in your directory:


WREPREGRO.DAT 	The first, hydrogen-, drug- and waterless coordinate file

WREINPGMT.DAT	Parameter file for PROGMT
WREJOBGMT.COM 	Job file for PROGMTL.EXE
WREOUTGMT.LIS 	The output from PROGMT
WREMTD.BIN	The binary topology file

WREINPGCH.DAT	Parameter file for PROGCH
WREJOBGCH.COM	Job file for PROGCHL.EXE
WREOUTGCH.LIS	The output from PROGCH
WREGRO.DAT	The coordinate file including drugs and hydrogens

IF USEWAT > 0 :

WREINPGWH.DAT	Parameter file for PROGCH
WREJOBGWH.DAT	Job file for PROGWH.EXE
WREOUTGWH.LIS	The output from PROGWH
WREWATGRO.DAT	Coordinate file of water oxygens without hydrogens
WREH2OGRO.DAT	Coordinate file of water oxygens with hydrogens

IF USEWAT > 1 :

WREINPBOX.DAT	Parameter file for PROBOX
WREJOBBOX.DAT	Job file for PROBOXL.EXE
WREOUTBOX.LIS	The output from PROBOX
WREBOXGRO.DAT	Coordinate file containing protein, drugs, water

IF USEWAT > 1 AND TOPOLOGY NOT NEUTRAL :

WREINPION.DAT	Parameter file for PROION
WREJOBION.DAT	Job file for PROIONL.EXE
WREOUTION.LIS	The output from PROION

IF USWAT > 1 AND TOPOLOGY NOT NEUTRAL :

WREINPGM2.DAT	Parameter file for PROGMT
WREJOBGM2.DAT	Job file for PROGM2L.EXE (identical copy of PROGMTL.EXE)
WREOUTGM2.LIS	The output from PROGMT
WREMTD10.BIN	The binary topology file (overwrites previous version)

IN all cases there is also WRETWOGRO.DAT, which is used as input for EM/MD.

Be aware that the project number is coded in all these files.

Energy minimization (WRUNEM)

In case you do not do too complex things, you can immediately use the command WRUNEM to do a GROMOS energy minimalisation run. If you type WRUNEM, WHAT IF just generates the job file WREJOB-EM.COM and the parameter file WREINP-EM.DAT. This file is pulled up in your favourite editor after conversion to human readable format by the program GET-EM. After you quit from editing, WHAT IF then executes PROEML.EXE to perform the EM run. WHAT IF expects that the file WREMTD.BIN is the topology file, and WRETWOGRO.DAT is the coordinate file. Also, WHAT IF expects that the parameters are already set correctly for this run. (See command PARAMS).

After the run you will find a few files in your directory:


WREGRO-EM.DAT	Formatted GROMOS coordinate file after minimalisation.
WREOUT-EM.LIS 	Formatted (descriptive) output from this EM run.
WRE-MDGRO.DAT0	Copy of WRE-EMGRO.DAT for administrative reasons.

These file names might be different depending on the parameters (see PARAMS).

Molecular dynamics (HEATUP/WRUNMD)

You can use the commands HEATUP/WRUNMD to do a special startup of a GROMOS molecular dynamis run. If you type HEATUP, WHAT IF just generates the job files WREJOB-MD.COM and the parameter files WREINP-MD.DAT. Only the first file is pulled up in your favourite editor after conversion to human readable format by the program GET-MD. After you quit from editing, WHAT IF then executes PROMDL.EXE to perform the MD run. In this run, the temperature is slowly increased, the temperature/pressure coupling constant slowly increased as well as the CUTOFF radius. This results in a slow increase of forces, preventing a crash of SHAKE. If you just want to perform a short MD run, this is also a good option. If WRUNMD is used, the simulation is initiated using velocities chosen from a Maxwellian distribution at the selected temperature. WHAT IF expects that the file WREMTD.BIN is the topology file, and WRE-MDGRO.DAT0 is the coordinate file. Also, WHAT IF expects that the parameters are already set correctly for this run. (See command PARAMS).

After the run you will find a few files in your directory:


WREGRO-MD.DATXX	Coordinate file (largest XX = the final one).
WREOUT-MD.LISXX		Formatted (descriptive) outputs from the HEATUP run.
WREINP-MD.DATXX	PROMDL input files
WREINP-MD10.COM_CONT	PROMDL input file for the continuation MD run
Trajectory files are also written, see MDCONT

XX = file identification number for each picosecond in HEATUP.

Molecular dynamics continuation (MDCONT)

If you have performed a startup run using HEATUP or WRUNMD, you are ready to perform a so-called MD continuation run, generating a long trajectory which you can analyse later. The MD run is executed from a script (WREJOB-MD.COM_CONT) one picosecond at a time. This is convenient, when you run out of diskspace or your machine crashes, you can only loose a maximum of 1 ps on CPU time. The MDSTEP parameter (see PARAMS) determines how long your MD run is. If you type MDCONT, WHAT IF looks in your directory for the LAST WRE-MDGRO.DATxx file and continues your simulation from there.

After the run you will find a few files in your directory:


WREGRO-MD.DATxx	Formatted GROMOS coordinate file after each ps of MD.
WREOUT-MD.LISxx		Formatted (descriptive) output of each ps of MD.
WRETRACRD.DATxx		Coordinates trajectory file of each ps of MD.
WRETRAVEL.DATxx		Velocities trajectory file of each ps of MD.
WRETRAENE.DATxx		Energies trajectory file of each ps of MD.

Fixing alpha carbons during a em or md run

Often one is rather certain about the fold, but not at all about the total structure. This is especially the case after building by homology from a structure with a high homology, or after making a few point mutants. In those cases it is wise to do the MD and/or EM with the alpha carbons fixed. There is no direct option to do this, but one can set the parameter FIXCA in the PAREMD menu to switch alpha carbon fixing on. The parameter FIXFRC then determines the force used by GROMOS to hold the alpha carbons in place. The maximum force allowed (at present) is 32000. This normally keeps the alpha carbons in long MD runs within 0.2 Angstrom of their original position, unless your structure is extremely bad.

Looking at output

All GROMOS programs create a user readable output file with results and the flow of the program in it. Also in case of errors, the error messages are written in this file. All these files have the extension .LIS. See one of the appendices for a complete list of default file names used by WHAT IF.

You can use the following commands to get these files in the editor at the screen: (of course you can also just type, edit or print them by hand)

Look at progmt output (SHOGMT)

The command SHOGMT will cause WHAT IF to bring the formatted user readable log file of the last PROGMT run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at progmt output (SHOGM2)

The command SHOGM2 will cause WHAT IF to bring the formatted user readable log file of the last PROGM2 run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at progch output (SHOGCH)

The command SHOGCH will cause WHAT IF to bring the formatted user readable log file of the last PROGCH run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at progwh output (SHOGCH)

The command SHOGWH will cause WHAT IF to bring the formatted user readable log file of the last PROGWH run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at proem output (SHO-EM)

The command SHO-EM will cause WHAT IF to bring the formatted user readable log file of the last PROEM run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at promd output (SHO-MD)

The command SHOMD will cause WHAT IF to bring the formatted user readable log file of the last PROMD run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at prommt output (SHOMMT)

The command SHOMMT will cause WHAT IF to bring the formatted user readable log file of the last PROMMT run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at probox output (SHOBOX)

The command SHOBOX will cause WHAT IF to bring the formatted user readable log file of the PROBOX run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Look at proion output (SHOION)

The command SHOION will cause WHAT IF to bring the formatted user readable log file of the PROION run in the editor. You can of course also type, edit, or print this output file by hand. See the appendices for a list of GROMOS related default file names used by WHAT IF.

Parameters for wre-gromos

The several WHAT IF - GROMOS preprocessor related options have their own parameter menus available. This chapter give a short description of the parameters that can be changed in order to influenze the behaviour of the program.

Parameters for GROMOS (PARAMS)

The command PARAMS brings you to the menu from which you can change the parameters for GROMOS. You can change the following parameters:

LEVUSE

This parameter determines the flow of the WREGRO option: Just create decks? Edit all decks? Run them when ready? When LEVBUSE > 0, the programs GET???.EXE and PUT???.EXE are used to cycle between unreadable GROMOS parameter files and human readdable format. The following values are allowed:

 0 : Create all files, don`t edit them, run them.
 1 : Create all files,  edit parameter files only, then run them.
 2 : Create all files, edit parameter/job files, then run them

 
MINTYP

Determines the way the minimization steps are determined. Steepest descent or conjugate gradient.

 1 : Steepest descent
 2 : Conjugate gradient

STEPS

This parameter determines the maximal number of steps. If the minimization is completed before this number of steps is reached, minimization is also stopped. STEPS can range from 1 till 500.


NEWGRD

In case you use the conjugate gradient method for minimization, this parameter determines after how many steps a new gradient correction will be performed. NEWGRD can range from 1 till 10.


ISHAKE

This parameter determines whether the bond lengths are constrained or not.

 0 : Do NOT use SHAKE.
 1 : Use SHAKE for hydrogens only
 2 : Use SHAKE for all bonds

MINDIF

The minimization stops as soon as the energy difference between two consequetive steps is less than MINDIF. MINDIF can range from 0.001 till 1.0.


STPSIZ

This is the step size (only in case you use steepest descent?) with which the minimization starts. This stepsize will be updated during the minimization. STPSIZ may range from 0.001 till 0.05.


MAXSTP

The stepsize during the minimization procedure (only in case of steepest descent?) is continuously automatically being updated. However, the step size is not allowed to exceed MAXSTP. MAXSTP may range from 0.01 till 0.1.


FIXCA

This parameter determines whether alpha carbons will be forced towards their original position or not. This parameter must be set before the WREGRO option is executed. 0 : Don't fix alpha carbons. 1 : Do fix alpha carbons.


FIXFRC

This parameter determines the force with which alpha carbons are held in place. See the GROMOS writeup for a description. Normal values are 1000 till 32000.


HTSTEP

This parameter determines in the length of your initiation MD run (see HEATUP/WRUNMD). Default is 5, use HEATUP and HTSTEP=25 for a realy gentle (but slow) heatup of your system.


MDSTEP

This parameter determines the number of ps in the continuation MD-run. (1-10000).


TEMP

This parameter determines the temperature during an MD-run (1.0-999.9).


TEMPER

This is the maximal deviation from the temperature set with the TEMP parameter. If the average temperature differs more, temperature rescaling will be performed.


TRAJEC

This parameter determines whether trajectories are written out during an MD run or not. Trajectories are always written unformatted. the allowed values are:

 0 : do not write any trajectories to file (default)
 1 : only write the coordinate trajectories to file
 2 : write the coordinates and the velocities to file
 3 : write coordinate, velocity and energy trajectories

Coordinate trajectories are written in the file WRETRACRD.DAT. Velocity trajectories are written in the file WRETRAVEL.DAT. Energy trajectories are written in the file WRETRAENE.DAT.

At present WHAT IF can only follow up with coordinate trajectory movies.


TRASTP

Allows you to specify the number of timeframes to skip each time before writing a timeframe to the trajectory file.

Parameters for adding waters (PARBOX)

The command PARBOX brings you in the menu from which you can change the parameters related to usage of waters in GROMOS runs.

At present there are no parameters implemented yet.

Special features

This paragraph holds some GROMOS related WHAT IF options that were hard to place in any category.

Checking coordinates and nomenclature (GCHECK)

The command GCHECK will cause WHAT IF to loop over all residues in the soup and check for the presence of some typical GROMOS errors. These errors are the swapping of the CH3-groups in valine and in leucine. When detected, the errors will be corrected.

Creating torsion angle restraint input cards

If you want to run torsion EM or MD with torsion angle restraints, you have to add one card for every angle to the input deck for PROEM or PROMD. The command TRSFIL creates a file with the correct format, but more important also the correct atom numbers (!!), for all phi, psi, and omega angles in a range of residues.

You will need to have the molecule you want to use this option on in the soup. You also need to have this same molecule as a GROMOS coordinate file. WHAT IF needs this to make a correspondence between the GROMOS atom order and the IUPAC atom order. You will be prompted for the GROMOS file, the number of the corresponding molecule in the soup, the range of residues in this molecule for which you want to get the restraint cards created, and the name of the restraint file. You will also be prompted for three force constants. These are the force constants for phi, psi, and omega respectively. The last two parameters on the restraint card are just arbitrary set to some numbers which allow for easy editting.

Limitations

When WHAT IF activates PROGMT, it only allows for the usage of one protein chain, and the following drugs:

          GROMOS
name      number        description

HEME        41          heme group (charge-2, acidic groups deprotonated)
FMNO        42          flavin mononucleotide (oxidized, deprotonated at
                        FN5 and FN1; charge-1 OPOHO2-)
FMNS        43          

         etc. see GROMOS writeup


MTH         83          methanol  (neutral)
H2O         82          water     (neutral)

SO4         68          SO4 ion   (charge-2)
ZN          76          zinc      (charge+2)
NA          77          sodium    (charge+1)
CL          78          chloride  (charge-1)
CA          79          calcium   (charge+2)
MG          80          magnesium (charge+2)

Other groups can be generated automatically with DAVADRUG during WREGRO.

WHAT IF assumes that both the N-terminus and the C-terminus are not blocked. That means the N-terminus automatically gets three H-atoms and the C-terminus an O-atom attached to it. Of course you can change this during WREGRO.

There are several ways of working with coordinate files etc (formatted or unformatted in all kinds of combinations). WHAT IF has chosen one of these combinations, and uses that one systematically (formatted).

It is NOT possible (yet) to use more than one peptide chain in a GROMOS run.