shahid nayeem wrote:
I couldn't get you. Does it means that for pre-positioning say 40
molecules of Arginine do I need to create 40 pdb of different coordinate
then combine it with pdb of protein and then use pdb2gmx. I want to use
different number of free positively charged Arginine molecule in
simulation box along with protein.
shahid nayeem
Treat the system like you would any other "normal" protein. Run pdb2gmx on a
coordinate file of a single molecule and proceed with building your system,
which can include replication (i.e. genconf to get multiple molecules), genbox
(to add other molecules and solvent), and genion. For systems with different
numbers of arginine, simply alter the corresponding line in the [molecules]
directive of the topology that pdb2gmx wrote.
-Justin
On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 11/08/2011 7:24 PM, shahid nayeem wrote:
Hi Justin
I prepared a box of SOL and arginine Hydrochloride. But when I
solvate my protein with this box now the positively charged
arginine is as solvent and this causes problem in grompp. It gives
error like "No such Molecule types ARG" etc. Solvating arginine
with water and preparing a box was without error. which forcefield
in gromacs has inbuilt .itp file for free amino acid which I can
include in my .top file.
See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains.
Pre-position the non-water molecules, use pdb2gmx, solvate.
Mark
Shahid Nayeem
On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shahid nayeem wrote:
Dear All I am trying to find the topology and parameterof
free Arginine Hydrchloride molecule in gromacs force-field
format. Developing it in Pro-Drg will not serve as I will
need some other parametrization tool to check it charges.
If someone can help, I will be grateful.
Isn't this just a protonated arginine (normal state for
neutral pH) with a chloride counterion? There's nothing
special about it, just run a coordinate file through pdb2gmx
with the force field of your choice.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
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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