Dear Prof. RossThank you for your help.Hereis I have attached my qm2_param.h file and the first part of the output.I have changed the PM3 parameters for the zinc ion.I look forward to hearing from you.Thanks in advanceS. Bill
--- On Tue, 9/2/10, Ross Walker <ross.rosswalker.co.uk> wrote:
From: Ross Walker <ross.rosswalker.co.uk>
Subject: RE: [AMBER] QM/MM new parameters
To: "'AMBER Mailing List'" <amber.ambermd.org>
Date: Tuesday, 9 February, 2010, 12:14
Hi Bill,
What changes did you actually make to the reference info?
You say that you added an ion, so did you actually create a new atom
parameterization or did you replace an existing atom?
If you can attach your qm2_parameters.h file with the changes highlighted
and also the modifications you made inside the qm2_print_references routine
then I can tell you if this was done correctly. Including your output file
would also be helpful.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of s. Bill
> Sent: Monday, February 08, 2010 3:54 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] QM/MM new parameters
>
> Dear AdrianIs there any option to print out the used PM3
> prameters?Thanks for your helpS. Bill
>
> --- On Mon, 8/2/10, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
>
> From: Adrian Roitberg <roitberg.qtp.ufl.edu>
> Subject: Re: [AMBER] QM/MM new parameters
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, 8 February, 2010, 23:40
>
> create a molecule with your ion and compare the results between your
> 'new' version and the original one.
>
> That should tell you which one it is using.
> a.
>
>
> On 2/8/10 3:32 PM, s. Bill wrote:
> > Dear AMBERI have implemented new PM3 parameters for one ion inside
> qm2_params.h, and I have recompiled AMBER. Aslo, I have changed the
> #REFERENCE: title for that ion.After using the new parameters I have
> adoubt about using the new parameters where I found my QM/MM out put
> says
> > 3.1 QM CALCULATION INFO-------------------------------------------
> -------------------------------------
> > QMMM: SINGLET STATE CALCULATIONQMMM: RHF CALCULATION, NO. OF DOUBLY
> OCCUPIED LEVELS = 84
> > | QMMM: Parameter sets in use:| QMMM: C : J.J.P.STEWART, JCC, 10, 209
> (1989)
> > Here, I found the original reference title (NOT the modified one,
> where I have changed this title).Is that indication of using the
> original PM3 parameters?How can I ensure Sander used my implemented PM3
> parameters?Thanks in advanceS.Bill
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> -- Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
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