[gmx-users] .top file from .gro file
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 20 01:19:30 CEST 2009
sunny mishra wrote:
> Hi Mark and Justin,
>
> Thanks for the valuable advise and I want to do the last test but before
> I proceed I just want to make sure If I am doing everything correct.
>
> I got the 1K4C_cleanCG.seq file using grep command like this
>
> grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq
>
> Now my next step is to get the .ssd file for 1K4C_cleanCG.pdb which I
> cannot get and in that case I have to use 1K4C_clean.pdb in order to get
> .ssd file.
>
> And If i am correct here then my next step would be to get the .itp file
> for 1K4C_cleanCG. So my last question is that when I will use seq2itp.pl
> script which .seq file should I use and which .ssd file should I use to
> get the output .itp file. I mean this....
>
> seq2itp.pl 1K4C_cleanCG.seq 1K4C_clean.ssd > 1K4C_cleanCG.itp
>
> OR
> seq2itp.pl 1K4C_clean.seq 1K4C_clean.ssd > 1K4C_clean.itp
>
> In the first command I don't think I can get the .ssd file(
> 1K4C_cleanG.ssd ) so thats why I am using 1K4C_clean.ssd. Now I dnt
> know if I am doing this wrong or correct but before proceeding i want to
> ask you guys to correct me at this point.
>
The .seq file should not depend at all on anything to do with the structure; the
amino acid sequence is invariant. You can download the FASTA sequence from the
PDB and use that (accounting for any missing terminal residues); it shouldn't
make a difference.
-Justin
> Thanks,
>
> Sunny
>
> On Wed, Aug 19, 2009 at 6:54 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
> 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 <http://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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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