Re: [AMBER] Restraint on certain atoms during MD

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 22 Apr 2020 16:33:19 +0000

Is this what you suggest?

restraintmask = ':1,:2-272.CA,C,N :273-274',

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________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, April 22, 2020 11:52:00 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Restraint on certain atoms during MD

I think you need a : before the residue number or it may be interpreted as
an atom number



On Wed, Apr 22, 2020 at 11:41 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:

> Hello Prof Simmerling
>
> I think I messed up the restraints
> So my protein has 284 C-alphas, 284 carbonyl carbons, 284 backbone amide
> nitrogen atoms, 12 atoms in my isopropanol, 6 atoms in NME and 6 atoms in
> ACE aps
> SO my total atoms restrained should be 284+284+284+12+6+6= 876
> I m getting 853 restrained only..
> Not sure what and where is the error?
> Any suggestions will be super useful.
> Thank you all.
>
>
>
>
>
> 22 April 2020 11:34
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Restraint on certain atoms during MD
>
> Thanks Prof Simmerling,
> Actually I m manually checking out the output file to see if that works
>
> This is what I found!
> Let me cross check to see if I have all atoms considered or not
>
>
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
> Mask :1-2,3-286.CA,C,N,287; matches 853 atoms
>
>
>
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
> Sent: 22 April 2020 11:28
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Restraint on certain atoms during MD
>
> 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
> > Windows 10
> >
> > 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 - 10:00:02 PDT
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