[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Thu Aug 20 00:30:25 CEST 2009
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 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
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...
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)
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.
Thanks a lot,
Sunny
On Wed, Aug 19, 2009 at 6:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> sunny mishra wrote:
>
>> Hi,
>>
>> I checked both the files they match exactly but still I get the same error
>> message that .gro file and .top file dnt match. I dnt know how to proceed
>> now.
>>
>>
> Well, something has to be wrong, or else grompp wouldn't complain. You say
> you've checked the .top, but have you also checked the contents of any
> relevant .itp files that are #included within it?
>
> -Justin
>
> Sunny
>>
>> On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra <mishra.sunny at gmail.com<mailto:
>> mishra.sunny at gmail.com>> wrote:
>>
>> Ok..I will see that and let you know. Thanks for the help though.
>>
>> Sunny
>>
>>
>> On Tue, Aug 18, 2009 at 8:12 PM, Mark Abraham
>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>> sunny mishra wrote:
>>
>> I did the same but again i get the same error..something
>> like this
>>
>> awk -f atom2cg_v2.1tryout.awk 1K4C.pdb > 1K4C_cg.pdb
>>
>> (This generated 1K4C_cg.pdb file)
>>
>> genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro
>>
>> (produced 1K4C_cg.gro)
>>
>> 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.
>>
>> :-) genbox (-:
>>
>> Option Filename Type Description
>> ------------------------------------------------------------
>> -cp 1K4C_cg.pdb Input, Opt! Structure file: gro g96
>> pdb tpr tpb tpa
>> -cs spc216.gro Input, Opt., Lib. Structure file: gro
>> g96 pdb tpr tpb
>> tpa
>> -ci insert.gro Input, Opt. Structure file: gro g96
>> pdb tpr tpb
>> tpa
>> -o 1K4C_cg.gro Output Structure file: gro g96
>> pdb
>> -p topol.top In/Out, Opt. Topology
>> file
>>
>> Option Type Value Description
>> ------------------------------------------------------
>> -[no]h bool no Print help info and quit
>> -nice int 19 Set the nicelevel
>> -box vector 10 10 10 box size
>> -nmol int 0 no of extra molecules to insert
>> -try int 10 try inserting -nmol*-try times
>> -seed int 1997 random generator seed
>> -vdwd real 0.105 default vdwaals distance
>> -shell real 0 thickness of optional water
>> layer around solute
>> -maxsol int 0 maximum number of solvent
>> molecules to add if
>> they fit in the box. If zero
>> (default) this is
>> ignored
>> -[no]vel bool no keep velocities from input
>> solute and solvent
>>
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/aminoacids.dat
>> WARNING: masses will be determined based on residue and atom
>> names,
>> this can deviate from the real mass of the atom type
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/atommass.dat
>> Entries in atommass.dat: 178
>> WARNING: vdwradii will be determined based on residue and
>> atom names,
>> this can deviate from the real mass of the atom type
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/vdwradii.dat
>> Entries in vdwradii.dat: 28
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/dgsolv.dat
>> Entries in dgsolv.dat: 7
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file
>> /usr/local/gromacs/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Reading solute configuration
>> MEMBRANE PROTEIN
>> Containing 1127 atoms in 534 residues
>> Initialising van der waals distances...
>> Writing generated configuration to 1K4C_cg.gro
>> MEMBRANE PROTEIN
>>
>> Output configuration contains 1127 atoms in 534 residues
>> Volume : 1000 (nm^3)
>> Density : 53.8545 (g/l)
>> Number of SOL molecules: 0
>>
>>
>> gcq#69: "I Want to Know Right Now" (Meatloaf)
>>
>>
>> After that ;;;;;;;;;;;;;;;;;;;;;;;
>>
>> grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10
>>
>> :-) G R O M A C S
>> (-:
>>
>> Gallium Rubidium Oxygen Manganese Argon Carbon
>> Silicon
>>
>> :-) 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_cg.gro 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.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.9#
>> 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.top, line 15]:
>> System has non-zero total charge: 4.000000e+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_cg.gro, 1127)
>> does not match topology (1K4C.top, 1166)
>> -------------------------------------------------------
>>
>>
>> That's a pretty explicit error message. Go and look at the
>> molecule and atom ordering in the two files and see where they
>> don't match.
>>
>> Mark
>>
>> _______________________________________________
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>>
>>
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>>
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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
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> Please search the archive at http://www.gromacs.org/search before posting!
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