Re: [AMBER] Restraint on certain atoms during MD

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Wed, 22 Apr 2020 15:41:28 +0000

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 - 09:00:03 PDT
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