I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box shahid nayeem
On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > 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. > > -Justin > > On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham > <mark.abra...@anu.edu.au<mailto: >> mark.abra...@anu.edu.**au <mark.abra...@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<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 <jalem...@vt.edu >>> <mailto: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 <http://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 >>> <mailto: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 >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> >>> Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> >>> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> > -- > ==============================**========== > > 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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