[gmx-users] (no subject)

Hi, I am studying polyglutamine regarding to my Ph.D work. Now my sequence is NH3+ -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-Q-COO-. I would like to cap the N and C terminal with the protecting groups CH3CO and NHCH3 instead of NH3+ and COO- respectively (i.e. CH3CONH-Q-Q-Q-Q-Q-CONHCH3). I am using GROMACS sof

[gmx-users] (no subject)

Hi How do I built the terminals of a peptide withe ACE and NHMe i.e.CH3CO and NHCH3 respectively. please suggest. My sequence is -Q-Q-Q-Q-Q-Q-Q-Q-Q-Q- M. Baskar. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] (no subject)

Hi, I am using GROMACS 4.0 for simulating a peptide having 5 residues.  I have built the sequence using pymol and capped the peptide with CH3CO and NHCH3 at its N and C terminal respectively and save in pdb file format.  The pdb file was used to produce *.gro and *.top files using pdb2gmx ff G43

[gmx-users] (no subject)

Hellow, My sequence was processed with SPDBV which add NH3 and COO- at the Nterminal and Cterminal respectively thereby MD simulation was carried out using GROMACS versions of  3.3.2 and 4.0.  The system was working well. Now I would like to add protecting groups i.e.acetyl group (CH3CO) and Nmet

[gmx-users] (no subject)

Hi  I want to add acetyl group at the N and C  terminal of my protein.   i.e. CH3-C=O NH QQQ NH CH3 by removing the NH3+ and COO- at the N and C terminal. Please suggest what steps I have to follow. regards M. Baskar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.