Re: Cyclopeptide: connectivity between the first and last residues

From: List (zheng042003_at_yahoo.com)
Date: Tue Sep 30 2008 - 19:08:44 CDT

Thanks both Jerome and David very much for the helpful information.  

I tried to figure out from psfgen usage description the right format to apply the patch, but   psfgen doesn't recognize my format.  What I have is:
      first none
      last none
plus the following:

      patch 2  9
where 2 and 9 are the resid of the first and last residues
or
      patch 2:AAAA  9:AAAA
where AAAA is the segid.

Your help will be very much appreciated,

Shirley

--- On Mon, 9/29/08, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
From: Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
Subject: Re: namd-l: Cyclopeptide: connectivity between the first and last residues
To: "David Tanner" <dtanner_at_ks.uiuc.edu>
Cc: zheng042003_at_yahoo.com, namd-l_at_ks.uiuc.edu
Date: Monday, September 29, 2008, 6:31 PM

On Mon, Sep 29, 2008 at 4:36 PM, David Tanner <dtanner_at_ks.uiuc.edu> wrote:
> Shirley,
>
> 1) You are allowed to edit your .psf file.

You certainly are, but I in most cases, I would recommend against it.
Instead, you can look up the "patch" statement of psfgen, as well as
the patch residues (PRES) LIG1, LIG2 and LIG3 in the charmm topology
file for proteins (assuming that you use charmm).

Best,
Jerome

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