Re: [AMBER] Restraint on certain atoms during MD

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 22 Apr 2020 16:45:20 +0000

I am so sorry working with 2 different proteins in 2 separate folders!
Sorry I meant this
restraintmask = ':1,2,:3-286.CA,C,N :287',
Residue 1 is isopropanol
Residue 2 is ACE cap
Residue 3 to 286.CA,C,N protein atoms(backbone)
Residue 287 NME cap
********************************************************************************
Still does not work
I need 876 atoms restrained, that is not happening...

From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 22 April 2020 12:40
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Restraint on certain atoms during MD

you've changed the residue numbers so I don't really know if this is right.
I suggest making adjustments and testing them to see what atoms are
selected.
this email in the archive might also be useful

http://archive.ambermd.org/201702/0412.html

On Wed, Apr 22, 2020 at 12:33 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:

> Is this what you suggest?
>
> restraintmask = ':1,:2-272.CA,C,N :273-274',
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> ________________________________
> 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 - 10:00:03 PDT
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