Subject: Re: Amber 4.0 help

From: [email-masked] (Brad Isbister)
Date: Wed, 4 May 94 03:36:50 -0400

Thanks to all of you who replied!  The fact that so many of you recognized my
error suggests that everyone else does this at least once. ;)

A summary of my question:

When I tried to use AMBER 4.0 to minimize a solute in a periodic box of water,
the program hadd a fatal error and gave the message:

     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE :    0    2    1    1    2

A summary of the answer:

Don't use SHAKE constraints before the initial minimization.  The constraints
on bond lengths by the SHAKE algorithm can conflict with the minimization forces
from strong VdW repulsion (too close).  Once SHAKE is turned off, everything
should work out fine.  To use SHAKE in MD, turn it on AFTER the initial
minimization.  Once the extreme VdW contacts have been eliminated, SHAKE
constraints will not cause any conflicts.

Further questions about AMBER can be answered through the AMBER mailing list:

>From [email-masked]
>
>There is a mail reflector for users and people interested in
>Amber. A major part of the traffic is the bugfix announcements.
>
>Mail sent to the reflector is automatically sent to all who have 
>joined the list.
>
>You can address all members by sending mail to either of the
>following addresses:
>
>        [email-masked]
>        [email-masked]
>
>and mail to either
>
>        [email-masked]
>        [email-masked]
>
>for administrative requests.

---------------------------------Clip N Save------------------------------------
Brad Isbister					Duke University
[email-masked]				Department of Chemistry
Computational/Biophysical chemistry		E.J. Toone group