Dear all,
I hvae used ANTECHAMBER & GAFF of Amber generate a .prmtop and .prmcrd of
a small molecular(XK263, a inhibitor of HIV-1 PR). I want to use ffamber99 in
Gromacs-3.3.1 to do a simulation of it, but I can't get the force field of the
molecular used in Gromacs.
On the Homepage of A
Dear Chris,
I have done similar calculation. Look at the supporting
info for http://dx.doi.org/10.1021/jp068587c. If you find
anything useful for you feel free to contact me.
Best regards
Vojtech Spiwok
Message: 1
Date: Wed, 25 Apr 2007 15:39:53 -0400
From: Chris Neale <[EMAIL PROTECTED]>
Su
Message: 2
Date: Tue, 6 Mar 2007 01:53:07 -0500
From: "Karthikeyan Pasupathy" <[EMAIL PROTECTED]>
Subject: [gmx-users] .GRO and .TOP files editing
To: "Discussion list for GROMACS users"
Message-ID:
<[EMAIL PROTECTED]>
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I have a polymer mole
Dear Luisa
The web tool propKa http://propka.chem.uiowa.edu/
might be useful in prediction of protonation states
of your protein at givven pH. Simulation with a
constant pH (with dynamic protonation state
assignment) was reported and might be an idea
for further gromacs development.
Vojtech
He
Dear gromacs gurus
I wonder to know if there is some
straightforward way to implement
angle, dihedral and possibly other
constraints to the pull code, beside
distance constraints. Any idea would
help.
Sincerely
Vojtech Spiwok
---
Ing. Vojtech Spiwok, PhD.
De
Dear Peter
Unfortunately, carbohydrates require special
parametrization of torsions and therefore you
should not use PRODRG topologies.
Vojtech Spiwok
ICT Prague
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Hi gmxions,
I have found out the eigen vectors computed of from a protein’s
simulation. Now I want to project
coordinates of entire simulation on to eigen vectors to see the
collective , anharmonic motion of that protein.
And doing so for wild and mutant protein, I expect to trace
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