[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Thu Aug 20 02:39:44 CEST 2009
Hi Mark,
I am sorry that I was not accurate in my scripts and I will not repeat this
mistake again. Justin advised me that if the atoms are missing in .itp file
and .gro file (Some of them are actually missing) then I have to model the
atoms back in the ORIGINAL PDB file but I din't quite get him. Can you help
me out with this that how to model the original PDB file (1K4C) before I
proceed.
Thanks,
Sunny
On Wed, Aug 19, 2009 at 8:25 PM, Mark Abraham <Mark.Abraham at anu.edu.au>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.
>>
>
> Justin's advice was also very sound. If your model lacks relevant atoms,
> you have more work to do. Surely the MARTINI scripts should be providing
> some warnings here?
>
> I got the 1K4C_cleanCG.seq file using grep command like this
>>
>> grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq
>>
>
> Nobody's interested in what your command was "like". This also was not your
> command, since you've added a space to make "1K4c_clean CG" and still not
> given it a filename suffix. Write a script so you've got a reliable record,
> or copy and paste from your terminal. Accuracy and reproducibility are
> critically important.
>
> Mark
>
> 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
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
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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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>>>
>>
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>>
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