Hi,
I think the problem here is that you need to disable the angle
calculation by setting 'angle -1' (the manual says set angle 0 which
is a typo). So:
donor mask :1.O1P
acceptor lig N13 N13
hbond distance 3.5 time 2 series PO_lig out PO_lig.dat angle -1
That should work.
-Dan
On Tue, Feb 5, 2013 at 11:00 PM, DEBOSTUTI GHOSHDASTIDAR
<debostutighosh.gmail.com> wrote:
> Hi...
>
> Thanks for your reply.
> 'lig' is not the real name of the residue, used it as an example.
>
> I executed ptraj using prnlev 3 and it does identify the donors and
> acceptors correctly, but finds no interaction between them.
>
> I then used 'O20 H21' (atoms in my 'lig') as the acceptor and it
> worked, however when I used O20 O20 as acceptor, once again it showed
> no interaction.
>
> Thanks in advance for your help
>
> On 2/5/13, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Hi,
>>
>> On Tue, Feb 5, 2013 at 6:07 AM, DEBOSTUTI GHOSHDASTIDAR
>> <debostutighosh.gmail.com> wrote:
>>> When I followed that, however, I did not get any
>>> output, although I know there is interaction between the two atoms.
>>>
>>> Here's my input:
>>>
>>> donor mask :1.O1P
>>> acceptor lig N13 N13
>>
>> Is your residue name really "lig"? I only ask because it's unusual to
>> have an all lower-case residue name and residue selection is
>> case-sensitive.
>>
>> If you're certain that an N13 atom in "lig" comes within 3.5 Ang. of
>> :1.O1P (maybe from a prior distance calc?), I would suggest you re-run
>> ptraj on a small subset of frames with the print level set above 0
>> (i.e. "prnlev <N>") to make sure your atom selections are being read
>> properly and to give you some more info as to what ptraj is doing,
>> e.g.:
>>
>> trajin mdcrd 1 10
>> prnlev 3
>> donor mask :1.O1P
>> acceptor lig N13 N13
>> hbond distance 3.5 time 2 series PO_lig out PO_lig.dat
>>
>> Good luck,
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Debostuti
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 06 2013 - 10:00:02 PST
