[gmx-users] Arginine_Hydrochloride topology
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 12 13:02:59 CEST 2011
shahid nayeem wrote:
> 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
Treat the system like you would any other "normal" protein. Run pdb2gmx on a
coordinate file of a single molecule and proceed with building your system,
which can include replication (i.e. genconf to get multiple molecules), genbox
(to add other molecules and solvent), and genion. For systems with different
numbers of arginine, simply alter the corresponding line in the [molecules]
directive of the topology that pdb2gmx wrote.
> On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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.
>> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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