Dear AMBER Users,
I have a question about the hydrogen bonding facility in ptraj. When you use
the "series" keyword to specify an output file to print time-series-related
information, would there be another directory where this file is written to?
I ask because I think I've specified enough memory for the facility.
Here are my input lines:
*trajin ../../production1.traj.gz*
*...*
*trajin ../../production200.traj.gz*
*
*
*center :1-73 mass origin*
*image origin center*
*donor mask :2.N7*
*
*
*hbond distance 3.5 angle 160 solventneighbor 6 solventacceptor Na+ Na+ Na+
series HDVr.dat out HDVr.out print 0.0*
HDVr.dat is never printed, and this is typically what I see in HDVr.out:
*BOND SUMMARY:*
* Data was saved to series A1+N7_Na+.dat, output to file A1+N7_Na+.out,
*
* data was sorted, intra-residue interactions are NOT included,*
* Distance cutoff is 3.50 angstroms, angle cutoff is 160.00 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*
* ---------------- ---------------------------------
-------------------------------------*
Thank you all in advance,
Kamali Sripathi
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Received on Thu Mar 17 2011 - 19:00:02 PDT
