[gmx-users] Normal Mode analysis

Hello everyone, I am trying to do normal mode analysis for a protein using Gromacs. Can anyone point me out towards a sample mdp file that I could edit for this purpose? Thanks Ajit B. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

Subject: Re: [gmx-users] simulating Ubiquitinated protein

Thanks David, I could edit the specbond.dat and thus pdb2gmx could make the bond between the desired residues. However, still there are two problems.. 1) Once the bond is formed the C-terminal glycine cannot be defined as a terminal one, but pdb2gmx treats it as a terminal residue and thus modifi

[gmx-users] simulating Ubiquitinated protein

Hi I am trying to do MD simulation of a ubiquitinated protein. (C-terminal linked to a lysine residue via an isopeptide bond). But I am not being able to define the isopeptide link. can someone help me out in this? Ajit B. ___ gmx-users mailing list