Re: [AMBER] Restraint on certain atoms during MD

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 22 Apr 2020 11:27:40 -0400

that seems close to what you have in the mask (which is quite different
from the original one). My only concern is that the "N,287" part doesn't
look like it would work properly.


On Tue, Apr 21, 2020 at 3:02 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:

> Yes Prof Simmerling,
> I wanted whole of 1,2, protein backbone atoms deoted by 3-286.CA,C,N and
> whole of 287...
> 2 and 287 are my ACE and NME caps, and residue 1 is my ethanol molecule
> tethered to a particular spot on my protein.
> Did the get my atom masks as needed?
> Thanks
>
>
>
>
>
>
>
> ******************************************************************************************************************************************************
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
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> From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
> Sent: 21 April 2020 14:59
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Cc: david.case.rutgers.edu<mailto:david.case.rutgers.edu>
> Subject: Re: [AMBER] Restraint on certain atoms during MD
>
> to me it looks like those are different atom selections, just something to
> keep in mind (did you want all of residue 1?)
>
>
> On Tue, Apr 21, 2020 at 2:56 PM Debarati DasGupta <
> debarati_dasgupta.hotmail.com> wrote:
>
> >
> > Hi Prof Case
> > That was not the issue, I corrected it , we do not need “:”
> >
> > This format worked
> >
> > ntr = 1, restraintmask = ':1-2,3-286.CA,C,N,287', restraint_WT = 20,
> >
> >
> >
> >
> ***********************************************************************************************************************************************************
> > From: David A Case<mailto:david.case.rutgers.edu>
> > Sent: 21 April 2020 14:55
> > To: AMBER Mailing List<mailto:amber.ambermd.org>
> > Subject: Re: [AMBER] Restraint on certain atoms during MD
> >
> > On Tue, Apr 21, 2020, Debarati DasGupta wrote:
> > >
> > >This is my restraintmask = ':1,:2-272.CA,C,N,:273,:274',
> >
> > Try removing the "," after "N".
> >
> > ...dac
> >
> >
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Received on Wed Apr 22 2020 - 08:30:02 PDT
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