AMBER Archive (2004)

Subject: Re: AMBER: TER in amber

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Thu Feb 12 2004 - 12:08:29 CST

I emailed out the prmtop file about one hour ago. I don't know whether
mail refector accepts it or not, because it's about 10M bytes. If you
tell me which part you want to look at, I can copy that part and email
it.

Best,
Lishan

On Thu, 2004-02-12 at 11:56, David A. Case wrote:
> 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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu