[gmx-users] Arginine_Hydrochloride topology
msnayeem at gmail.com
Thu Aug 11 11:24:29 CEST 2011
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.
On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul <jalemkul at 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 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
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