AMBER Archive (2004)

Subject: RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Dec 14 2004 - 11:53:58 CST

Dear Ilyas

Have you applied the two QMMM bug fixes to your amber 8 installation and
re-compiled sander.QMMM? See

http://amber.scripps.edu/bugfixes/8.0/bugfix.13

And

http://amber.scripps.edu/bugfixes/8.0/bugfix.26

The latter one should not effect the tutorial results as it only deals with
problems with link atoms.

Check if the tests pass once you have applied the fixes. Make
test.sander.QMMM.

You should be able, if you use exactly the same files as on the tutorial,
reproduce the tutorial results to within round off error. Can you post me
your output file.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Ilyas Yildirim
> Sent: 13 December 2004 20:35
> To: amber_at_scripps.edu
> Subject: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation
>
> Hi all,
>
> While I was following the Workshop 2004, tut. #6, I
> encountered a problem
> with the QMMM MD simulation part. The minimisation procedure of QMMM
> method gives the following error:
>
> ...
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> ***** REPEATED LINMIN FAILURE *****
> ...
>
> I even have copied/pasted the files for QMMM min. part given in the
> tutorial, and still got the same error. The input files are
> here (given in the
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_
> Six/index.htm
> webpage)
>
> divcon.in
> -------------------
> CARTESIAN PM3 CHARGE=0 &
> STANDARD DIRECT
> END_COORD
> -------------------
>
> min_qmmm.in
> -------------------
> Initial min of our structure QMMM
> &cntrl
> imin=1, maxcyc=500, ncyc=200,
> cut=20, ntb=0, fcap=1.5,
> ifqt=1, nqt=12, idc=0
> /
> 1 2 3 4 5 6 7 8 9 10 11 12
> END
> END
> -------------------
>
> md_qmmm.in
> -------------------
> 300K constant temp QMMMMD
> &cntrl
> imin=0, ntb=0,
> cut=20, fcap=1.5,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=1000, dt=0.001,
> ntpr=1, ntwx=1,
> ifqt=1, nqt=12, idc=0
> /
> 1 2 3 4 5 6 7 8 9 10 11 12
> END
> END
> ------------------
>
> The NMA.prmtop and NMA.inpcrd files are exactly the same
> files given in
> the above given website. Anyone having any idea why I am getting these
> errors? I have installed AMBER 8 to a DELL 5100, P4 laptop,
> with a SUSE
> Linux 9.1 Personal Edition. Thanks in advance...
>
> Ciao,
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, Office B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
>
> --------------------------------------------------------------
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