[gmx-users] .top file from .gro file
mishra.sunny at gmail.com
Wed Aug 19 01:17:01 CEST 2009
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
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
My topology file looks like this
; Include forcefield parameters
; Include protein
[ system ]
[ molecules ]
; compound # mols
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 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.
On Tue, Aug 18, 2009 at 7:00 PM, Justin A. Lemkul <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.
>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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