[gmx-users] CHARMM nonbonded parameters and grompp output

Mark Abraham 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
>> as
>>>> well.
>>>>>  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
>> is
>>> incomplete because it contains only 40 lines, with C as the first entry and
>> HT
>>> as the last entry.  There are no entries for any atom types other than
>> carbon
>>> 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 
version numbers.

> 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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