AMBER Archive (2006)

Subject: RE: AMBER: How to build 1,4-dimethyl benzene with amber9

From: Ross Walker (
Date: Fri Apr 28 2006 - 18:46:23 CDT

Hi Martin,

> I understood that the sequence command constructed the new unit from
> the internal coordinates of the fragments.
> Am I mistaken believing it should at least reproduce the geometry
> from the prep file for each fragment,
> though it may get the inter-fragment conformation wrong?

I believe that it would do. I think I misunderstood your previous email. I
didn't realize you were getting the structure of the individual fragments
was coming out wrong. Can you possibly send me your prepin files so I can
try it out myself.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to