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 <[email protected]>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 <[email protected]> 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 >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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