[gmx-users] .top file from .gro file
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 20 00:54:18 CEST 2009
In addition to everything Mark said, also realize that there may be a
fundamental problem in everything you are doing: there are missing atoms in the
original 1K4C structure. If you have not modeled them back in, the appropriate
CG particles will not necessarily all be placed in your CG structure, but the
topology will be written such that it expects all the correct atoms to be there.
At first glance, Arg117 is going to cause headaches - it is missing all atoms
beyond CB, and since CG and NE are necessary for MARTINI's definition of an ARG
residue, you can bet this will be a problem.
-Justin
Mark Abraham wrote:
> 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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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