[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Thu Aug 20 01:35:51 CEST 2009
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>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> 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
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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>>> Please search the archive at http://www.gromacs.org/search before
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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!
>> 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
>>
>
>
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