[gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

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

On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham <Mark.Abraham at 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 <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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
>
>
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