Hi George,
I) I guess you mix up donor and acceptor in these commands ... even if it
sounded contradictory to me too.
II) Also your "SER" residue name might be refering to more than one serin and
applying a mask would be more specific.
gl Alexander
________________________________
Von: George Tzotzos <gtzotzos.me.com>
An: AMBER Mailing List <amber.ambermd.org>
Gesendet: Montag, den 13. September 2010, 15:55:13 Uhr
Betreff: [AMBER] ptraj hbond analysis
Hi everybody,
I've completed production MD on a receptor/ligand complex. The ligand has a
hydroxyl moiety which is shown in crystallographic models to form a hydrogen
bond with the hydroxyl group of a receptor Serine.
I have visualised the MD trajectory in Chimera and observed the type of bonding
described above as well as hbonds between the ligand OH and a receptor Thr OH.
I'm trying to calculate the H-bond occupancy for these two different types of
conformation using the following script (hbond.in)
trajin prod14ns.mdcrd
donor SER O H
donor THR O H
acceptor BOM O
hbond distance 3.5 angle 120.0 includeself donor acceptor neighbor 2 series
hbond
The output I get is:
PTRAJ: Successfully read in 200 sets and processed 200 sets.
HBOND SUMMARY:
Data was saved to series hbond,
data was sorted, intra-residue interactions are included,
Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.00
Dumping schematic of time series after each h-bond, key follows:
| . - o x * . |
0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
angle lifetime maxocc
The program fails to produce hbond statistical analysis. I can only assume that
the above script is wrong.
Any suggestions on the syntax or other points for troubleshooting?
Many thanks in advance
George
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Received on Mon Sep 13 2010 - 08:00:03 PDT
