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 - 07:00:03 PDT
