[gmx-users] obtaining a pdb after a simulation with ffamber

Dear users, I've been running a MD simulation on a protein using ffamber94 (from amber ports with gmx 3.3.1). After the run, I extracted and minimized an average structure. I then converted the lowest energy structure (.gro) from the minimization in a pdb file with trjconv, but turns out som

[gmx-users] weird behavior of genion in gromacs4

lecules in topology file (H1_opls.top) by 37 opls_407 and 44 opls_401 ions"? Thank you very much Serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Harvard Medical School Channing Laboratory EBRC 609 221 Longwood Avenue Boston, MA 02115 (tel) 617-732-8586 The informa

[gmx-users] doubt about the ffencadv.rtp

improper_X_X_N_X instead of -C CA N H improper_X_X_N_X am I right, or am I overlooking something? Thank you very much, Cheers, Serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Harvard Medical School Channing Laboratory EBRC 609 221 Longwood Avenue Boston, MA 02115

[gmx-users] doubt about the oplsaa topology

day to all... serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Harvard Medical School Channing Laboratory EBRC 609 221 Longwood Avenue Boston, MA 02115 (tel) 617-732-8586 The information transmitted in this electronic communication is intended only for the person or entit

[gmx-users] Glycam and gromacs

Hello everybody, I would just like to renew a question that was made more or less one year ago and that received no answer: Has anyone tried (and succeeded...) to use Glycam (with Amber ff) in Gromacs? Thank you, Cheers, Serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Ha

[gmx-users] error in grompp

this behavior? Thanks a lot Cheers, Serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Harvard Medical School Channing Laboratory EBRC 609 221 Longwood Avenue Boston, MA 02115 (tel) 617-732-8586 The information transmitted in this electronic communication is intended only for

[gmx-users] T-Coupling group

6 but I thought the T-coupling groups were defined in the index file, not the topology. Anybody knows what I am doing wrong? Thanks a lot Serena -- Serena Leone, Ph.D. Brigham and Women's Hospital Harvard Medical School Channing Laboratory EBRC 609 221 Longwood Avenue Boston, MA 0

[gmx-users] charge in genbox

Hello I've recently started using Gromacs, and I'm trying to model a charged polypeptide. I built it either with maestro or pymol, I generated the .top and .gro, and according to the topology files it has the expected charge (+5). When I try to generate the water box, after running genbox and bef