From: Jason Swails <>
Date: Thu, 19 Sep 2013 06:41:25 -0400

On Thu, Sep 19, 2013 at 4:15 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <> wrote:

> Dear Jason
> NAN= No Atom Name

Actually NaN means "Not a Number." []
 It is an almost universal sign of some type of problem (either user or

EPB/EGB = the electrostatic contribution to the solvation free energy
> calculated by PB or GB respectively
> ECAVITY = nonpolar contribution to the solvation free energy calculated by
> an empirical model

You misunderstood me. I'm aware of what all of these terms mean. What is
important when debugging is _which_ terms had NaN as their respective
values? Since the solvation free energy is NaN, that means either the
polar solvation term (EPB/EGB) or the non-polar solvation term (ECAVITY,
ESURF, EDISPER) must be NaN (or both). Knowing this gives clues about
where to look for problems. Of course you also omitted the G gas term from
your email, so there could be problems there as well.

I have visualized generated mdcrds using VMD...what i feel is
> there are abnormalities in ligand geometry and also few in receptor..

This does not help, as it leaves me to "guess" what the 'abnormalities' are
(and what you would consider 'normal'). For instance:
 and are two
different 'abnormalities' which have quite different root causes and
solutions. A picture is worth more than any number of words in this case.

As general advice when asking questions of this nature, you will receive
helpful answers far faster if you provide a good amount of details. Show
the full output (not just lines you find troubling, because those are often
not helpful by themselves). Show the exact commands that you used and any
error messages or outputs that were produced. Also say how you tried to
fix or debug it, and what you learned (or think you learned) in the
process. Otherwise, the first few days will be spent trading emails of
this sort...


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 19 2013 - 04:00:03 PDT
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