RE: AMBER: Amber7 nmropt

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 16 Feb 2005 13:55:40 -0800

HHmmm, this is different from the Amber 8 manual to which I was refering:
 
NMROPT = 0 no nmr-type analysis will be done;
> 0 NMR restraints/weight changes will be read
              = 2 NOESY volume restraints or chemical shift restraints will
be read as well.
 
So perhaps the behaviour has changed between amber 7 and 8 (or just that the
manual has been updated correctly). Perhaps someone more familiar with this
area of the code could comment further...
 
All the best
Ross
 

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|\oss Walker

| Department of Molecular Biology TPC15 |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Markus W. Germann
Sent: 16 February 2005 13:41
To: amber.scripps.edu
Cc: Markus W. Germann
Subject: Re: AMBER: Amber7 nmropt


Hi Ross

yes there were no NOESY volumes nor shift restraints. .. Just rdc and the
usual NOE/J based restraints. What surprised me was that rcd restraints were
supposed to require nmropt=2 (7 manual)... so at that point one worries what
is going on.

tx


On Feb 16, 2005, at 4:32 PM, Ross Walker wrote:



If you had no NOESY volume chemical shift restraints defined then nmropt = 2
would just have been treated as nmropt > 0 which in the absence of the above
restraints being defined is the same as nmropt=1. Hence the same results.
 
I hope this makes sense.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | 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.
 


From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Markus W. Germann
Sent: 16 February 2005 13:09
To: amber.scripps.edu
Cc: Markus W. Germann
Subject: AMBER: Amber7 nmropt

This is regarding the nmropt statement in Amber 7

We updated an older rdc restraints file from Amber 6 to 7 and 8.

By accident, I left nmropt=1 for an Amber 7 run, subsequently I rerun this
with nmropt=2 (as per manual)
The data from both runs are identical and both contain alignment restraints.

Does anyone have any insights on this?

Tx

Markus W. Germann, Ph.D.
Department of Chemistry
Georgia State University
Phone: 404 651 1576



Markus W. Germann, Ph.D.
Associate Professor
GCC Distinguished Cancer Scholar
Director of Graduate Studies
Department of Chemistry
Georgia State University
Phone: 404 651 1576

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