On 5/21/13 12:53 PM, Rama Krishna Koppisetti wrote:
Hi..,Mark
but it is within the same molecule , not in inter-molecules.
That's what distance restraints are designed for. Please refer to the manual
for topology syntax and explanation of the relevant parameters.
-Justin
On Tue, May 21, 2013 at 11:36 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote:
Yes. Check out the manual first!
Mark
On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti <
ramkishn...@gmail.com> wrote:
Hi Mark,
Is there anyway to define NMR distance restraints in MD simulations to do
refinement for the complex structure.
On Tue, May 21, 2013 at 10:11 AM, Mark Abraham <mark.j.abra...@gmail.com
wrote:
You can't - the atoms must be part of the same [moleculetype]. The good
news is that a [moleculetype] can have whatever you want in it, so you
can
have more than one molecule. The bad news is that you'll have to be
cunning
with renumbering atoms in the merged [moleculetype] and there's no
tools
that do that. (Or maybe there's a smart-alec trick using the pull code,
but
I have no idea what.)
Mark
On Tue, May 21, 2013 at 4:20 PM, Rama <ramkishn...@gmail.com> wrote:
Dear Gromacs users,
How to define distance restraints between two molecules(protein and a
lipid)
in a topology file.
Thanks..
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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