On Wednesday 04 August 2004 03:48 pm, Ross Walker wrote:
> Dear Bud,
>
> > A question about sander.QMMM (AMBER8) input.
>
> First question, have you applied bugfix.13? If not, do this first of all
> before you do ANY QMMM calcs.
>
Hi Ross,
I _think_ I did (I applied bugfix.all, IIRC), but I will check
explicitly tonight.
> The charge you specify in divcon.in should be just the charge on the QM
> system. Bare in mind however that any bond you break will have hydrogen
> atoms added in the QM region. E.g:
>
>
> H H H H QM region = C1 and C2 H H
> HC1-C2-C3-C4H ------------------------> HC1-C2H Charge =0
> H H H H H H
>
> Hence check if you are breaking bonds and where. Then for every bond you
> break add a hydrogen on the QM section and at the end of it see what you
> are left with. Then calculate charge of this QM piece and set that in the
> divcon.in file.
>
Hmmm... That was my interpretation (in analogy with the full
DivCon version, MOPAC, etc). I'll email you my input files Fri
(I'm out tomorrow, and it is 6:50PM here at home). Briefly,
though, the QM section of the run that failed is a dinucleotide + a
carboxylate + a protonated amine, total charge of -1 (including
the internucleoside phosphate):
5'O-nside1-3'O-PO_2-5'O-nside2-3'O (flanked by the rest of the DNA
treated via MM). Plus the carboxylate and amine (residues on the
enzyme). Two link hydrogens cap the 5'- and 3-hydroxyl oxygens
(plus several for residues on the enzyme). CHARGE=-1 => "odd
number of electrons in closed shell calculation" (or some such).
The system that ran to completion with no error message left out
the central PO_2, so would have two more link hydrogens in place
of the phosphorus and two oxygens. CHARGE=0 => runs OK, but
3'-sugar ring opens between C3' and C4'. Oops!
So it could be the bugfix problem, unless I've missed something.
Thanks! I'll send the files via private email on Fri.
Bud
> If you still have problems please email me your input files and I'll take
> a look and see if I can get it to run.
>
> All the best
> Ross
>
> /\
> \/
>
> |\oss Walker
> |
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
--
M. L. Dodson bdodson.scms.utmb.edu
409-772-2178 FAX: 409-772-1790
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Aug 05 2004 - 02:53:01 PDT
