Dear All
I have a situation I was trying to evaluate Hbond command for tracking Na+
ion interactions with RNA. My ptraj input file looks like this
trajin /md_center_Na.x 1 1000 1
donor mask :RG.O6
donor mask :47-111 ( these are my sodium ions)
acceptor mask :Na+ :Na+
hbond series h2 time 2.0 distance 5.0 out hbond_ions.dat solventdonor Na+Na+
solventacceptor Na+Na+Na+
and my out file prints no data in this it looks like this as shown below.
Please suggest how to obtain the ion interaction using Hbond. I have tried a
numerous permutationa and combinations but could not get ion interaction.
BOND SUMMARY:
Data was saved to series h2, output to file hbond_ions.dat, time
interval is 2.00
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 5.00 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
---------------- ---------------------------------
-------------------------------------
~
With Regards,
Abhishek Singh
Doctoral student
Material Science and Engineering
North Carolina State University
Raleigh, NC 27695-7907
Phone # 5179272418
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 22 2009 - 13:00:02 PDT
