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. Shahid Nayeem
On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul <jalem...@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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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