AMBER Archive (2000)

Subject: 2 questions

From: mkf7_at_cornell.edu
Date: Wed Nov 15 2000 - 17:00:54 CST

Hello,

I am learning how to use AMBER6 and I have two questions - they might be
related.

(1) In running simple MD, I often get an error called "Trace/BPT Trap".
Is there a likely reason for getting this error?

(2) I am interested in doing the following simple MD simulation:
load a pdb
create the .top and .crd files needed to go on to sander
run simple md to get a picture of flexibility of the eqm structure

(the protein is made of 2 chains). I
have fixed my cys and his groups and they seem to be read fine. When
AMBER reads the pdb, it seems to put extra atoms on terminal groups; the
extra atoms do not have a noticeable TYPE. My going into the pdb file
created by AMBER (after it read the original pdb) and deleting these
lines allows AMBER to read it and create the .top and .crd files.
However, I feel that I am doing something wrong here. Am I supposed to
use connect atoms or something?

Thanks for your help
Mike Fenwick