Dear Amber users,
My doubt remains...so Im posting this query again...
I intend to obtain lifetime and occupancy data for electrostatic
interaction between two atoms, using the hydrogen bond analysis
facility of ptraj. However, both the atoms are not electron acceptors,
i.e, neither have hydrogens attached to them. In one of the mail
threads it was mentioned that in such a case, acceptor and acceptorH
can be the same atom. 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
hbond distance 3.5 time 2 series PO_lig out PO_lig.dat
The output file shows no interaction although the donors and acceptors are
recognised correctly. As suggested earlier, i checked ptraj output with
prnlev 3 and it showed the acceptors are being read correctly. I also tried
to find interaction using another set of acceptor atoms: O20 H21, and
interactions were there . However when i used O20 O20, once again there
were no interactions. I also increased the distance cutoff to 5 and even
10A. That too didnt work.
Don't know where I am going wrong. Please help.
Thanks
--
Debostuti
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 06 2013 - 09:30:02 PST
