[gmx-users] (no subject)

[munubas at yahoo.com]

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.