AMBER Archive (2004)

Subject: Re: AMBER: TER in amber

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 12 2004 - 10:56:45 CST

On Thu, Feb 12, 2004, Lishan Yao wrote:

> I use ambpdb to convert a restrt file to a pdb file. If you look at the
> pdb file I get, it is kind of strange because ambpdb put TER inside
> MET159. It's supposed to be between GLU158 and MET159.

We would need to see your prmtop file to figure this out. The ambpdb
program gets its information from that file, in different ways depending
on whether or not it is a periodic simulation.

Once we have the prmtop file, we could see whether ambpdb is making a
mistake or not. If not, we would have to peel the onion back one more
level, and try to figure out why the information in the prmtop file is wrong.

...regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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