Re: Hydroxyprolin force field.

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jan 26 2004 - 17:44:10 CST

Or even easier, look for a par_hyp.inp file in the same place you found
the top_hyp.inp file and add a new parameters line to your NAMD input.

-Jim

On Fri, 23 Jan 2004, Brian Bennion wrote:

> On Fri, 23 Jan 2004 ivan.vinogradov_at_utoronto.ca wrote:
>
> > Hello All,
> >
> > I am currently trying to minimize a collagen model.
> > Unfortunately (for minimization) it has a rather large number of HYP residues
> > in it.
> > Neither top_*.inp nor par_*.inp files available from charmm website seem to
> > contain HYP data.
> > Search on the web netted no sufficient results.
> > I have found a top_hyp.inp file in this m-list archive but now NAMD complains
> > about missing bonds in par*.inp file.
> > What would be a solution to the problem?
>
> Easy
> Measure the bond lengths in the structure and add them to the par.inp
> file!!
>
> Regards
> Brian
>
> >
> > Cheers, Ivan.
> >
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:02 CST