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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