[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Thu Aug 20 01:23:09 CEST 2009
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> 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>> 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
>
> ========================================
> _______________________________________________
> 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!
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