Dear David,
Thank you for the specifying the manual pages in chapter 24.1.
Unfortunately the mentioned text is very brief
and insufficient for a new user as me.
In fact the whole amber manual is written in reference book
style for experienced users but not for beginners.
There is an example in the addressed chapter :
restraint = "distance( (45) (49) )"
but nothing is explained how to set the required interatomic distance value
(3.0 A for instance), and how to set also the force constants values in the
cited above command.
I would appreciate if you could give a detailed example of input file for
minimization
and MD simulation accounting interatomic distance restraints for one or two
atomic pairs.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Fri, Jul 3, 2015 at 3:26 PM, David A Case <david.case.rutgers.edu> wrote:
> On Fri, Jul 03, 2015, Michael Shokhen wrote:
> >
> > Unfortunately I failed to find in Amber manual and archive
> > a clear example of the command lines how to set the interatomic distance
> > restraint
> > and to add it to the md.inp script file for productive MD simulation.
>
> These are termed "NMR" restraints (for historical reasons) in Amber jargon.
> See Section 24.1 ("Distance, angle and torsion restraints") in the 2015
> Amber Reference Manual for details.
>
> ....dac
>
>
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Received on Sun Jul 05 2015 - 05:30:03 PDT
