[gmx-users] .top file from .gro file
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 20 01:38:07 CEST 2009
As I said before, the original PDB file is missing atoms. You have to model
them back in before you do anything else, otherwise MARTINI will expect them to
be there and they won't be!
-Justin
sunny mishra wrote:
> Hi Justin and Mark,
>
> I just realized that I have some missing atoms in my .gro file when I
> compared with .itp file and may be this is causing the problem. The
> atoms which are missing what should I do with them. Should I delete both
> from .itp and .gro file OR do i have to add in my .gro file and if I
> have to add them then how?
>
> for example in my .itp file there are 2 ILE but in my .gro file there is
> only 1 ILE. So should i add another ILE in my .gro file or delete 2 ILE
> from .itp and 1ILE from .gro. Thanks in advance.
>
> Sunny
>
> On Wed, Aug 19, 2009 at 7:23 PM, sunny mishra <mishra.sunny at gmail.com
> <mailto:mishra.sunny at gmail.com>> wrote:
>
>
> Alright. Sounds good to me. let me check that out and i will let you
> know the progress.
>
> Thanks,
>
> Sunny
>
>
> On Wed, Aug 19, 2009 at 7:19 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>
> <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
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list.
> Use the
> www interface or send it to
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
> (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use
> the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list