Re: [gmx-users] Arginine_Hydrochloride topology

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

Re: [gmx-users] Arginine_Hydrochloride topology

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

Re: [gmx-users] Arginine_Hydrochloride topology

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

Re: [gmx-users] Arginine_Hydrochloride topology

shahid nayeem wrote: 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

Re: [gmx-users] Arginine_Hydrochloride topology

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

Re: [gmx-users] Arginine_Hydrochloride topology

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.

Re: [gmx-users] Arginine_Hydrochloride topology

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

[gmx-users] Arginine_Hydrochloride topology

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. shahid Nayeem --