Re: [AMBER] Restraint on certain atoms during MD

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Tue, 21 Apr 2020 19:02:11 +0000

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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 21 2020 - 12:30:02 PDT
Custom Search