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)
>
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Debostuti
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Received on Tue Feb 05 2013 - 22:30:03 PST
