[AMBER] restraints in Targeted Molecular dynamics

From: siddesh southekal <siddeshonline.gmail.com>
Date: Tue, 22 Feb 2011 11:20:52 +0100

Dear AMBER users,

I am trying to run Targeted molecular dynamics (TMD ) simulations. I want to
target certain transmembrane helices of the protein strucuture ( say helix
1 : RES xxx to yyy ; helix 2 : RES aaa to bbb ) and thus I want to use these
helices as reference / target for the TMD by use of the group input :

*RES xxx yyy
RES aaa bbb

However i think this can be used only be used with *ntr =1 *flag
if its turned off , this group input / or the restraintmask will
subsequently not be read.So i am not sure how to turn on restraint without
use of ntr flag !
is there any other flag i should be using for the group input to be read ? [
i do not want to apply positional restraint ]

As per the manual we cannot use restraintmask and tgtfitmask together .Are
the residues / atoms mentioned in the tgtfitmask targeted ??
Hence ,only Input to the tgtfitmask would be sufficient ?

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Received on Tue Feb 22 2011 - 02:30:04 PST
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