Re: Cyclopeptide: connectivity between the first and last residues

From: List (zheng042003_at_yahoo.com)
Date: Mon Oct 06 2008 - 11:58:17 CDT

Just want to say that the "patch LIG" method works.   

One think I want to point out is that the "patch LIG" entry" should NOT be put inside the segment XXX {...} block.  Otherwise psfgen wouldn't recognize it.

Shirley

--- On Tue, 9/30/08, List <zheng042003_at_yahoo.com> wrote:
From: List <zheng042003_at_yahoo.com>
Subject: Re: namd-l: Cyclopeptide: connectivity between the first and last residues
To: namd-l_at_ks.uiuc.edu
Date: Tuesday, September 30, 2008, 8:08 PM

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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