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
>>
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>
>
>
> --
> -------------------------
> 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 - 10:00:06 PDT
