Dear Amber Users,
I am actually trying to calculate the intramolecular hydrogen bonds that
exist in a residue in my simulation system. However, I am failing to get any
output written. I know that intramolecular hydrogen bonds exist in the
molecule. I have confirmed this by calculating the distances and angles
using VMD by loading my output file from the simulation.
The following is my input file for hbond:
*trajin md3_im.mdcrd 1 100
donor mask :mer.O10
donor mask :mer.O11
acceptor mask :mer.O7 :mer.H19
acceptor mask :mer.O8 :mer.H20
hbond distance 3.5 angle 180.0 includeself series hbs out hbond.dat*
Following is the ptraj output:
*PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin md3_im.mdcrd 1 100
Checking coordinates: md3_im.mdcrd
PTRAJ: donor mask :mer.O10
Mask [:mer.O10] represents 10 atoms
PTRAJ: donor mask :mer.O11
Mask [:mer.O11] represents 10 atoms
PTRAJ: acceptor mask :mer.O7 :mer.H19
Mask [:mer.O7] represents 10 atoms
Mask [:mer.H19] represents 10 atoms
PTRAJ: acceptor mask :mer.O8 :mer.H20
Mask [:mer.O8] represents 10 atoms
Mask [:mer.H20] represents 10 atoms
PTRAJ: hbond distance 3.5 angle 180.0 includeself series hbs out hbond.dat
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 100 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md3_im.mdcrd) is an AMBER trajectory (with box info) with 100 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> HBOND saved to series hbs, output to file hbond.dat, inter-solvent
hbonds will not be included,
data will be sorted, intra-residue interactions will be included,
Distance cutoff is 3.50 angstroms, angle cutoff is 180.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 0.47 MB
donors: 20 acceptors: 20 frames: 100
Processing AMBER trajectory file md3_im.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100
PTRAJ: Successfully read in 100 sets and processed 100 sets.
Dumping accumulated results (if any)
PTRAJ HBOND dumping summary to file hbond.dat
*hbond.dat file contains the following summary:*
HBOND SUMMARY:
Data was saved to series hbs, output to file hbond.dat,
data was sorted, intra-residue interactions are included,
Distance cutoff is 3.50 angstroms, angle cutoff is 180.00 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
---------------- ---------------------------------
-------------------------------------
*
Please suggest me regarding how I can get my output written.
Thanks in advance.
-Sudha
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Received on Tue Jul 27 2010 - 07:30:03 PDT
