[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Thu Aug 20 01:11:25 CEST 2009
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.
Thanks,
Sunny
On Wed, Aug 19, 2009 at 6:54 PM, Justin A. Lemkul <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.organd
>>> 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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