[gmx-users] Regarding creating interface between two solvent at particular site

Hello I am trying to build a solvent box of two solvents. Water & octane. I want to create a interface at a particular site of the protein, as i am studying interfacial activation of Lipase's lid. Kindly suggest. Thanks Yuvraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.groma

Re: [gmx-users] No such moleculetype NA+

> [ atoms ] > ; idat typeres nr residu nameat name cg nrcharge > mass > 1CU1+1CU1CU 11 63.54600 > > [ moleculetype ] > ; molnamenrexcl > CU1 > > [ atoms ] > ; idat typeres nr residu name

[gmx-users] "freezegrps" concept

Hello I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic" as box with distance of 1nm b/w solute n box. Protein is going out of the box after equilibration step. Any solution? Should i use *freezegrps* option to restrict protein movement. Please provide some light to this

[gmx-users] Polyglycine simulation

I have to simulate polyglycine of length 20. Is there any software or server which can give me PDB input for polyglycine. Please help. Thanks -- Yuvraj Uboveja -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Regarding parameters of octane box in ffamber99sb - ildn

sults. >> >> I appreciate any advice on this! >> >> Thanks, >> Sebastian >> > > I can't see anything that looks wrong. Make sure you inspect the output of > grompp thoroughly for clues about how it's interpreting the .top file. You > may like t

[gmx-users] Parameterization

How to parametrize N-acetyl Glucosamine present in my PDB file with AMBER force field to use in GROMACS. Please suggest some solutions. Thanks -- Yuvraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww