[gmx-users] (no subject)

[Justin A. Lemkul]

munubas at yahoo.com wrote:
> 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.

Most force fields include capping groups.  You'll have to tell us exactly which 
force field you're trying to use, what files you modified (and with what), any 
relevant commands, errors, etc otherwise you'll get no useful advice.

-Justin

> 
> M. Baskar, Dept of Biophysics, Panjab University, Chandigarh, India.
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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