[gmx-users] .top file from .gro file

[Mark Abraham]

sunny mishra wrote:
> Hi Justin,
> 
> Thanks for the reply and here is the following which I am doing. I would
> appreciate if you can point out my errors.
> 
> 
> 1) I am working on 1K4C (KcSA) and i downloaded that from www.pdb.org and
> after that I cleaned the PBD file, removed all the HETATOMS and ATOMS with
> ligand A & B and also removed the TER atoms. So my cleaned PDB file i.e.
> (1K4C_clean.pdb) consists of atoms with ligands C and #of atoms are 765.
> 
> 2) After getting the 1K4C_clean.pdb I converted the atomic structure to CG
> structure using awk script...something like this
> 
> awk -f atom2cg.awk 1K4C_clean.pdb > 1K4C_cleanCG.pdb

Here you create 1K4C_cleanCG.pdb

> 3) Then I got the sequence of 1K4C_clean.pdb using vmd and saved that as
> 1K4C_clean.txt and with the help of the following command I got the .seq
> file...

But below you create your .itp starting from "1K4C_clean", which at 
least means you haven't copied your correct grep line, and might 
indicate the mismatch between your structure and topology.

> grep -A 1 1K4C_clean 1K4C_clean.txt > 1K4C_clean.seq
> 
> 4) Then using dssp I got the .ssd file for 1K4C_clean.pdb....
> 
> dsspcmbi 1K4C_clean.pdb 1K4C_clean.dssp
> dssp2ssd.py 1K4C_clean.dssp -o 1K4C_clean.ssd
> 
> 5) After preparing the secondary structure files I generated the MARTINI
> topology files like this :
> 
> seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp
> 
> 6) The next step is to make the topology file and I made like this.....
> 
> ; Include Martini Topology
> #include "martini_v2.1.itp"
> 
> ; Include protein topology
> #include "1K4C_clean.itp"
> 
> 
> [ system ]
> ; Name
> Membrane Protein
> 
> [ molecules ]
> ; compound       #mols
> Protein            1
> 
> 7) Then I made the .gro file using genbox.....
> 
> genbox -cp 1K4C_cleanCG.pdb -box 10 10 10 -o 1K4C_cleanCG.gro
> 
> (In the previous email as you said that I need to make the .gro file of CG
> structure of protein so I used 1K4C_cleanCG.pdb)

A .gro file is almost never essential. A structure file with a suitable 
periodic box can be.

> 8) Now I want to minimize the system.....
> 
> grompp -f em.mdp -c 1K4C_cleanCG.gro -p 1K4C_clean.top -maxwarn 10
> 
> and then error comes...........
> 
> :-)  G  R  O  M  A  C  S
> (-:
> 
>                    GROningen MAchine for Chemical Simulation
> 
>                             :-)  VERSION 4.0.5  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
> 
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
> 
>                                 :-)  grompp  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f         em.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c 1K4C_cleanCG.pdb  Input        Structure file: gro g96 pdb tpr tpb tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p 1K4C_clean.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o      topol.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   yes     Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                             sites
> -maxwarn     int    10      Number of allowed warnings during input
> processing
> -[no]zero    bool   no      Set parameters for bonded interactions
> without
>                             defaults to zero instead of generating an
> error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number
> of
> 
> atomtypes
> 
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Replacing old mdp entry 'unconstrained_start' by 'continuation'
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
> checking input for internal consistency...
> 
> NOTE 1 [file em.mdp, line unknown]:
>   For energy conservation with switch/shift potentials, rlist should be 0.1
>   to 0.3 nm larger than rcoulomb.
> 
> 
> NOTE 2 [file em.mdp, line unknown]:
>   For energy conservation with switch/shift potentials, rlist should be 0.1
>   to 0.3 nm larger than rvdw.
> 
> processing topology...
> Generated 0 of the 465 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'Protein'
> 
> NOTE 3 [file 1K4C_clean.top, line 15]:
>   System has non-zero total charge: 2.000000e+00
> 
> 
> 
> processing coordinates...
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: grompp.c, line: 362
> 
> Fatal error:
> number of coordinates in coordinate file (1K4C_cleanCG.pdb, 209)
>              does not match topology (1K4C_clean.top, 216)
> -------------------------------------------------------
> 
> I don't know where I have done the mistake...your help will be highly
> appreciable in this case.

Here you've got a 7-atom difference, and...

>>>            -------------------------------------------------------
>>>            Program grompp, VERSION 4.0.5
>>>            Source code file: grompp.c, line: 362
>>>
>>>            Fatal error:
>>>            number of coordinates in coordinate file (1K4C_cg.gro, 1127)
>>>                        does not match topology (1K4C.top, 1166)
>>>            -------------------------------------------------------

...here you're different by 39 atoms. That indicates a procedure that 
differed by more than just not adding solvent.

With a complex multi-step system preparation, you are much better served 
by writing the steps down in a shell script so that you really do things 
the same way every time. Science is still science, even on a computer, 
and your work must be reproducible. Moreover, then when you ask for 
help, you're not presenting contradictions and non sequiturs that 
frustrate attempts to help you :-)

In any case, my earlier advice still applies - it should be a matter of 
10 minutes work to compare your clean .itp and .gro to see what atoms 
are causing the problem. Then, work backwards.

Mark