yes you need to use the tgtfitmask and rmsmask- check the manual for
details.
On Tue, Feb 22, 2011 at 5:20 AM, siddesh southekal
<siddeshonline.gmail.com>wrote:
> 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
> END
> END*
>
> 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 ?
>
> Thanks,
> Siddesh
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Received on Sat Feb 26 2011 - 12:30:04 PST
