[gmx-users] Arginine_Hydrochloride topology

[Mark Abraham]

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 <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
>
>     -- 
>     ========================================
>
>     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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