AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Jul 03 2006 - 14:19:57 CDT

> I am running hbond analysis on a nuclear receptor steroid complex. My input
> file is as follows:
...

> > acceptor mask :UNK @O11,H12
> > acceptor mask :UNK @O26,H27

...you need to separate masks here, one for the O and one for the H's...

> > hbond print .05 series hbt

You likely want to output the results to a file...

hbond print 0.05 series hbt out hbond.dat

> 1> HBOND saved to series hbt,
> data will be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.05
> Estimated memory usage for this hbond call: 1690.06 MB
> donors: 198 acceptors: 207

For your data, it is estimated that it will require 1.7GB of RAM. Make
sure the machine has this much and that you have unlimited memory use
(from the shell, type unlimit memoryuse).

If you do not have this much memory, you will need to do it over multiple
runs (by reducing the number of donors/acceptors in each, i.e. one script
with half the donors and all the acceptors and the other script with the
other half of the donors with all the acceptors).

--tom

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