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
Received on Tue May 18 2010 - 09:00:05 PDT
