[gmx-users] .top file from .gro file
sunny mishra
mishra.sunny at gmail.com
Wed Aug 19 02:04:49 CEST 2009
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)
-------------------------------------------------------
On Tue, Aug 18, 2009 at 7:54 PM, sunny mishra <mishra.sunny at gmail.com>wrote:
>
> Alright sounds good to me. In order to make it sure once again....I have to
> do something like this...
> awk -f atom2cg.awk 1K4C.pdb > 1K4C_cg.pdb
>
> and then....to get the .gro file....
>
> genbox -cp 1K4C_cg.pdb -box 10 10 10 -o 1K4C_cg.gro
>
> and then......
>
> grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10
>
> AM I CORRECT?
>
> Sunny
>
>
> On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> sunny mishra wrote:
>>
>>> Hi Justin,
>>>
>>> I am using these commands...
>>>
>>> genbox -cp 1K4C.pdb -box 10 10 10 -o 1K4C.gro
>>>
>>> from here I can get my 1K4C.gro file.
>>>
>>> As far as CG structure of protein is concerned I can produce the CG
>>> structure using awk script like this..
>>>
>>> awk -f atom2cg.awk 1K4C.pdb > 1K4C_CG.pdb
>>>
>>> But after getting the CG structure its difficult to get the .itp file for
>>> 1K4C_CG.pdb because dssp does not produce .ssd files for CG structure of
>>> proteins and if I am not having .ssd file then i cant get 1K4C_CG.itp file
>>> so thats why I did not use awk script and I was just doing for the normal
>>> protein to test first.
>>>
>>>
>> You need the awk script to generate the CG structure. You use the
>> atomistic structure to get the .ssd information - you've done this
>> correctly.
>>
>> Here is the error------------
>>>
>>> grompp -f em.mdp -c 1K4C.gro -p 1K4C.top -maxwarn 10
>>>
>>
>> <snip>
>>
>>
>>> 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.
>>>
>>
>> Pay attention to these notes!
>>
>> 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.gro, 4534)
>>> does not match topology (1K4C.top, 1166)
>>>
>>>
>> Now this makes sense. You are using an atomistic structure (1K4C.gro)
>> with a CG topology. The structure input into grompp should be the CG
>> structure that comes from the awk script.
>>
>> -Justin
>>
>>
>>>
>>>
>>> On Tue, Aug 18, 2009 at 7:24 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>> sunny mishra wrote:
>>>
>>> Ok. Thanks but I am doing a small test to make the .top file and
>>> .gro files of fresh 1K4C protein structure without removing
>>> anything but when I run my grommp command to minimize it as I
>>> asked earlier as well it says number of atoms in the .top are
>>> not equal to .top file and as you said that without adding any
>>> other molecule I just have to fix the [molecules] section, but
>>> it doesn't fix.
>>>
>>> here are some details of my .top file which I created on my own
>>> after getting the 1K4C.itp file. I got 1K4C.itp file something
>>> like this..
>>>
>>> grep -A 1 1K4C 1K4C.txt > 1K4C.seq (This generates 1K4C.seq)
>>> dsspcmbi 1K4C.pdb 1K4C.dssp (gives 1K4c.dssp)
>>> dssp2ssd.py 1K4C.dssp -o 1K4C.ssd (this gives 1K4C.ssd)
>>>
>>> seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp
>>>
>>>
>>> <snip>
>>>
>>>
>>> and after that I produce my 1K4C.gro file from genbox or
>>> editconf and then when i run the command grommp it says that
>>> number of atoms in .gro
>>>
>>>
>>> What commands are you giving genbox/editconf? You've never invoked
>>> the awk script that converts an atomistic protein structure to CG
>>> (provided by the MARTINI folks). Could that be the cause of the
>>> disconnect? Without seeing the actual error message, the best
>>> anyone can do is guess.
>>>
>>> -Justin
>>>
>>> file are unequal to .top file. Since I am doing the simulation
>>> in vacuum I cannot add anything else. Don't know how to proceed.
>>>
>>> Thanks,
>>>
>>> Sunny
>>>
>>> On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul
>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>>
>>>
>>>
>>> sunny mishra wrote:
>>>
>>> Hi all,
>>>
>>> Is there anyway I can generate the .gro file from .top file
>>> without using the command pdb2gmx and editconf?
>>>
>>>
>>> A .top file is a topology - atomic descriptions; a .gro is a
>>> coordinate file. They are unrelated and therefore cannot be
>>> inter-converted.
>>>
>>> -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 <http://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 <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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>
>
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