[gmx-users] CHARMM nonbonded parameters and grompp output
Mark.Abraham at anu.edu.au
Fri Feb 22 06:03:03 CET 2008
Justin A. Lemkul wrote:
> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
>> Justin A. Lemkul wrote:
>>>>> The ffcharmmnb.itp file is incomplete, and I suspect ffcharmmbon.itp is
>>>>> Any idea what's going on?
>>>> No, since you haven't said why you think they're incomplete :-)
>>> Sorry, I sent that a bit too quickly, didn't I? I suspect ffcharmmnb.itp
>>> incomplete because it contains only 40 lines, with C as the first entry and
>>> as the last entry. There are no entries for any atom types other than
>>> and hydrogen.
>> Right, well that is far too short. HT should not even be the final H
>> atom-type. The code writes all of the [atomtypes] in the same foreach
>> loop, which is just dumping pre-constructed lines of text. The fact that
>> this has only written 40 of many more lines suggests the problem is
>> external to the script. Full file-system? Killed process? Try again?
> Yep, this one is a real stumper. My filesystem has 11.5 GB available on the
> partition I'm trying to write to, and I've tried a couple more times, using a
> fresh download of your scripts (just to be sure, even though I'm sure I haven't
> changed it). I know I haven't modified the .prm file in any way, and the
> process doesn't seem to be getting killed.
OK, that's weird. Can you mail me your .prm, and these output files
off-list, just to see if I can reproduce it. Likewise the perl script
> Perl version is 5.8.6 on Mac OS X 10.4.11, although I get the same output on an
> Ubuntu Linux machine running Perl 5.8.8. I don't know if that makes any
> difference, although I doubt it should.
> Is there anything I can do to diagnose this issue? Sorry to say I'm not fluent
> in Perl :-(
There is some debugging output available in the script by uncommenting
various things, but I can't see it being helpful for this problem, or in
the hands of someone inexperienced with Perl.
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