[gmx-users] .top file from .gro file
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 19 02:02:38 CEST 2009
sunny mishra 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
>
Or you can use editconf, but genbox will also work.
> and then......
>
> grompp -f em.mdp -c 1K4C_cg.gro -p 1K4C.top -maxwarn 10
>
> AM I CORRECT?
>
The only way to know is to try. In theory, yes, the above should work.
-Justin
> Sunny
>
>
> On Tue, Aug 18, 2009 at 7:44 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>>
> <mailto: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>
> <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> <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
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