It's boolean logic. Or means combine the groups
On Wed, Apr 22, 2020, 6:07 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Hi Daniel
> Why do I need a “OR” operator, should that not be “&” AND.. as I need all
> the masks as mentioned in my previous emails.
> Thanks for your reply
> Debarati
>
> ****************************************************************************************************************************************************************
> From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
> Sent: 22 April 2020 17:00
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] Restraint on certain atoms during MD
>
> Hi,
>
> On Wed, Apr 22, 2020 at 12:45 PM Debarati DasGupta
> <debarati_dasgupta.hotmail.com> wrote:
> > restraintmask = ':1,2,:3-286.CA,C,N :287',
>
> The colon after the comma after the 2 will cause the parser to choke;
> it's not valid syntax. You need to use the OR operator '|' if you want
> to combine 2 or more different masks. So you need:
>
> :1,2|:3-286.CA,C,N|:287
>
> You can simplify further by grouping all the residues that you want
> the whole residue selected together, e.g.
>
> :1,2,287|:3-286.N,CA,C
>
> Hope this helps,
>
> -Dan
>
> > 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 - 15:30:02 PDT
