[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

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

://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! -- Yuvraj Uboveja M.Tech. Bioinformatics IIIT Hyderabad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[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

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

To: YUVRAJ UBOVEJA yuvraj.ubov...@students.iiit.ac.in, Gromacs Users' List gmx-users@gromacs.org Date: Mon, 06 Dec 2010 07:31:08 -0500 Subject: [gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than 30 degrees Please keep all Gromacs-related correspondence on the gmx-users list. I

[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