You need to specify two masks for the acceptor command, one for the heavy
atoms and one for the hydrogens. Again, from the manual the acceptor command
is:
acceptor resname atomname atomnameH | mask mask maskH | clear | print
The relevant part here is "mask mask maskH". So you would need something
like
acceptor mask :1496-6496.O :1496-6496.H1
acceptor mask :1496-6496.O :1496-6496.H2
However, to just keep track of interactions of this residue with the solvent
you don't need to explicitly specify your water as a donor or an acceptor;
this should be taken care of with the solventdonor and solventacceptor
keywords of the hbond command. So you could do something like:
donor mask :1321.N=,O=,S=
hbond series hbt angle 120.0 distance 3.5 solventneighbor 100 solventdonor
SPC O solventacceptor SPC O H1 solventacceptor SPC O H2 hbfile
hbond_time.dat avgfile average_stat.dat solventhbonds
Please carefully read section 6.9 in the AmberTools 1.4 manual for more
information.
-Dan
On Tue, May 18, 2010 at 12:43 PM, Ganesh Kamath <gkamath9173.gmail.com>wrote:
> Hi,
>
> I tried this and I still get the same message as before.
>
> trajin mdcrd
> center origin
> image origin center
> acceptor mask :1496-6496.O=
> acceptor mask :1496-6496.H=
> donor mask :1321.N=,O=,S=
> hbond series hbt angle 120.0 distance 3.5 solventneighbor 100
> solventdonor SPC O solventacceptor SPC O H1 solventacceptor SPC O H2
> hbfile hbond_time.dat avgfile average_stat.dat solventhbonds
> go
>
>
>
> On Tue, May 18, 2010 at 11:32 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > I think the acceptor command requires the heavy and hydrogen atom masks
> to
> > be specified separately. From the manual:
> >
> > acceptor resname atomname atomnameH | mask mask maskH | clear | print
> >
> > So you need to split the mask you have into an O part and an H part. One
> > note, I think that the same number of atoms needs to be specified in the
> > mask and maskH part, so you would need to have two acceptor commands, one
> > for each hydrogen on each water. Alternatively if you don't care about
> > angles you can just put the 'O' mask twice which disables the angle
> > calculation.
> >
> > -Dan
> >
> > On Mon, May 17, 2010 at 5:25 PM, Ganesh Kamath <gkamath9173.gmail.com
> >wrote:
> >
> >> Hi all,
> >>
> >> I am trying to use the hbond utility and determine the possible
> >> hydrogen bonds between protein residue and
> >> water (SPC).
> >> I try defining the acceptor
> >> acceptor mask :1496-6496.O=,H=
> >> or even
> >> acceptor mask :SPC.O=,H=
> >> or
> >> acceptor SPC
> >>
> >> while executing this line it doesnt seem to detect the atoms and says
> >> "WARNING in ptraj, acceptor: Error in mask specification. Ignoring..."
> >>
> >> It seems to be giving me an output with the possible water
> >> interactions with protein residue but I am worried about the warning.
> >>
> >> Could some please help.
> >>
> >> thanks,
> >>
> >> ganesh
> >>
> >> SCRIPT
> >>
> >> trajin mdcrd
> >> center origin
> >> image origin center
> >> acceptor mask :1496-6496.O=,H= *****SPC water******
> >> donor mask :1321-1481.N=,O=,S= *****protein residues*****
> >> hbond series hbt angle 120.0 distance 3.5 solventneighbor 100
> >> solventdonor SPC O solventacceptor SPC O H1 solventacceptor SPC O H2
> >> hbfile hbond_time.dat avgfile average_stat.dat solventhbonds >EOF
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Postdoctoral Associate
> > SAS - Chemistry & Chemical Biology
> > 610 Taylor Road
> > Piscataway, NJ 08854
> > _______________________________________________
> > 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
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue May 18 2010 - 12:00:03 PDT
