rama david wrote:
Hi GROMACS friends,
I am trying to put to peptide close to each other..
with the help of -editconf -ci and -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
To solve problem I proceed as follow...
1. I make gro file , with the -editconf I make box and put molecule in
center
I get the box vectors and center co-ordinates.
2. then again with the help of editconf I make a another box of same vectors
but slightly different center co-ordinates.(Distance is as per my
requirement)
3 Now have two gro files of box molecule ,having same box vectors and
different
center.
4 I converted both gro files to pdb files ,and catenate them to make
single pdb file.
5 Now I get the two molecule close enough to form hydrogen bond..
but the problem is to convert it again into gro file and
generate topology
It is easier to not generate a topology from this file. If the peptides are
identical, run a coordinate file of *one* of them through pdb2gmx and obtain its
topology. Then simply update the number of protein molecules in the [molecules]
directive to reflect that the new system has two.
file , should I removed periodicity of molecule (As it showing the
periodic box in pymol)???
If it is , how to remove periodicity???
What periodicity do you want to remove? You have two peptides in a box, there's
nothing to do there.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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