AMBER Archive (2007)

Subject: Re: AMBER:

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 14 2007 - 10:27:48 CDT

On Fri, Aug 10, 2007, Steve Seibold wrote:
>
> I tried to send the attachments, but after one hour they have not showed
> up on the AMBER site and so, I am now sending the following message
> without the attachments.
>
> I have an unusual problem with xleap or when I make a pdb file using
> "ambdpb". When I load my initial pdb file (p010A.pdb) into xleap and
> save my topology and coordinate files WITHOUT water my output pdb files
> are fine. However, if I add waters and follow the same procedure (i.e.
> load p010A.pdb and make promtop and inpcrd files), I get very strange
> placements of the "TER" command when I construct a pdb file using
> "savepdb file file.pdb" or "ambpdb" commands. Basically it slices up my
> protein and the heme.

How big is the pdb file? Could you reduce its size to find a smaller example
that still shows the problem?

...thanks...dac

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