AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Dec 11 2009 - 21:39:55 CST

Hi Hashem,

> I'm having a problem running a QM/MM job. the job just stops running
> with no
> apparent errors. Looking at example output files for QMMM on the web,
> it
> seems that the job stops right when it tries to read in the QMMM
> residues.
> I'm not sure if this a problem with my input file or a problem with
> AMBER. I
> have included the output file (which also includes my input). Can
> anyone
> help?
...
> Initial minimization of structure QMMM
> &cntrl
>
> ntwx = 50, ntpr = 1, ntwr = 1,
> imin=1, maxcyc=1000, ncyc=100,
> cut=8.0, ntb=1, ntc=2, ntf=2,
> ifqnt=1
> /
> &qmmm
> qmmask=':1-2',
> qmcharge=0,
> qmtheory='PM3CARB1',
> qmshake=1,
> qm_ewald=1, qm_pme=1
> /
...
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals

A couple of questions. Firstly does this work if you do not use QMMM? I.e.
if you set ifqnt=0 does it run okay? It is possible that you are feeding
sander a nonperiodic inpcrd file but asking for periodic boundaries. This
can cause a hang.

Secondly, you are running this in parallel. On how many processors? Does it
work in serial?

If it only shows up in parallel then I suspect you may be hitting bug 6:

http://ambermd.org/bugfixes/10.0/bugfix.6

Did you apply all the bugfixes and recompile?

If not try this first and then get back to me if it still does not work with
the prmtop and inpcrd you are using.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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