[gmx-users] Arginine_Hydrochloride topology
Mark.Abraham at anu.edu.au
Thu Aug 11 11:45:13 CEST 2011
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.
Pre-position the non-water molecules, use pdb2gmx, solvate.
> Shahid Nayeem
> On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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 <http://vt.edu> | (540) 231-9080
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