Re: [AMBER] Restraint on certain atoms during MD

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 22 Apr 2020 17:04:17 +0000

Finally I got this
cpptraj -p complex_0_lamda_solvated.prmtop --mask ':1-2,:3-286.CA,C,N:287'|wc -l

This gives me 876 atoms I need for my mask!
Thank you so much Prof Simmerling.

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 12:48:25 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Restraint on certain atoms during MD

try the link I sent


On Wed, Apr 22, 2020 at 12:45 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:

> 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 - 10:30:02 PDT
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