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 software for this study. I have tried with GROMACS but its library has not been included with N Acety and N Methylamide at its N and C terminal. Due to this .gro file or .top file could not be made. I have even included the CH3CO group in the library. still it is not making sense to produce the .gro and .top file. I request you to suggest how to cap the above thereby to overcome this problem using GROMACS.
M. Baskar, Dept of Biophysics, Panjab University, Chandigarh, India. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
