Re: [AMBER] Fixing pdb files prepared in VMD, minor errors

From: David A Case <>
Date: Tue, 2 Jul 2013 13:37:29 -0400

On Tue, Jul 02, 2013, Hunter Brown wrote:
> I changed the OT1s to Os which fixed that problem. However after
> changing OT2 to OXT I am still running into trouble:
> FATAL: Atom .R<VAL 40>.A<OXT 17> does not have a type.

It looks like LEaP doesn't recognize Valine 40 as being a Cterminal residue.
Is it the last residue in the file? If not, is it immediately followed either
by a TER card, or by an ATOM record with a new chain id?

As Dan (I think) pointed out, you can use the "desc" command in leap to
examine the contents of each residue. Experiment with smaller pieces of the
file to help in debugging.


AMBER mailing list
Received on Tue Jul 02 2013 - 11:00:02 PDT
Custom Search