Dear Francois,
Thanks for the explanations!
What i mean is that, i have done resp calculations on 24 conformations and
can i average the resp charges?
As i read this from
http://q4md-forcefieldtools.org/RED/FAQ-I.php
"Do you average RESP results on many orientations?"
"Yes, we do average RESP results on 'different' orientations: we called it
multi-orientation-RESP fit by analogy to the multi-conformational RESP fit,
see below"
Or do i misunderstand your meaning?
how many conformations should be use to be useful? is that depends on the
molecule itself?
Pls advice. Thank you very much.
Regards,
Colvin
On Wed, Jun 30, 2010 at 3:15 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Colvin,
>
> Charge fitting is different from charge averaging!
> There is a discussion about this topic in the q4md-fft mailing list:
> See
>
> http://lists.q4md-forcefieldtools.org/wws/arc/q4md-fft/2010-05/msg00024.html
>
> Shortly:
> - When you do charge averaging for X orientations (and/or X
> conformations), you derive X charge sets based on X single orientation
> charge fits and then you average the X charge sets into a single one
> - When you do charge fitting based on X orientations, you derive a
> single set of charges based on X MEPs/X orientations
>
> Usually, in RESP charge derivation charge averaging is not used.
>
> You can use whatever number of conformations/orientations you want in
> RESP charge derivation. However, I wonder if 24! is really useful...
>
> regards, Francois
>
>
> > Dear Francois,
> >
> > by the way, can i just average the charges over the 24 conformations? Pls
> > advice.
> >
> > Thank you very much.
> >
> > On Wed, Jun 30, 2010 at 2:21 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Dear Colvin,
> >>
> >> I forgot a point:
> >> If you are interested in molecular orientation, in R.E.D.-III.4 the
> >> rigid-body reorientation algorithm has been rewritten allowing to
> >> study the impact of translation versus rotation (besides the
> >> re-orientation procedure originally defined in R.E.D. I).
> >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#Translate
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#Rotate
> >> versus
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#QMRAALGO
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#RBRAALGO
> >>
> >> Thus, any user can demonstrate by herself/himself the origin of the
> >> problem of charge reproducibility.
> >>
> >> regards, Francois
> >>
> >>
> >> > Dear all.
> >> >
> >> > I was trying generate force field parameter for a molecule with 134
> atoms
> >> > and 24 different orientations/conformations using GAFF, following the
> >> > tutorial provided from http://ambermd.org/antechamber/example.htmland
> >> > ambertools user manual.
> >> >
> >> > These are the steps used:
> >> >
> >> > 1. antechamber -i *.mol2 -fi mol2 -o *.com -fo gcrt (* = number
> >> corresponds
> >> > to 24 different orientations)
> >> > 2. run gaussian with the default input file generated from antechamber
> >> > 3. espgen -i *.log -o *.esp (extract out the esp)
> >> > 4. cat *.esp > all.esp (merge all the esp files into one)
> >> > 5. respgen -i *.ac -o step1.respin1 -f resp1 -n 24
> >> > 6. respgen -i *.ac -o step2.respin2 -f resp2 -n 24
> >> > 7. resp -O -i step1.respin1 -o step1.respout1 -e all.esp -t
> qout_stage1
> >> > (default resp input file from respgen)
> >> > 8. resp -O -i step2.respin2 -o step2.respout2 -e all.esp -q
> qout_stage1
> >> -t
> >> > qout_stage2 (default resp input file from respgen)
> >> > 9. antechamber -i 1.ac -fi ac -o resp.ac -fo ac -c rc -cf qout_stage2
> >> >
> >> >
> >> > My question is:
> >> >
> >> > 1. Are the procedure above correct?
> >> >
> >> > 2. if i use the first 3 molecules and above and concatenate the
> >> correspond
> >> > esp files for resp calculations, the charges are all the same.
> >> > for example, cat 1.esp 2.esp 3.esp > first3.esp --> respgen with -n 3
> >> --->
> >> > do resp calculation using first3.esp and read qout_stage2 to 1.ac(same
> >> > apply to 1-4molecules, 1-10molecules and 1-24 molecules, the charges
> are
> >> the
> >> > same --> charge set A)
> >> >
> >> > if i use only 2 molecules (molecule 1-2), the charges are different
> >> compared
> >> > to the above case -->charge set B.
> >> >
> >> > if i use the last 3 molecules and below, the charges are the same as
> well
> >> > but are different with case 2.
> >> > for example, cat 24.esp 23.esp 22.esp > last3.esp --> respgen with -n
> 3
> >> --->
> >> > do resp calculation using last3.esp and read qout_stage2 to 1.ac(same
> >> apply
> >> > to 24-21molecules, 24-15molecules and 24-1 molecules, the charges are
> the
> >> > same --> charge set C)
> >> >
> >> > I am confuse with this...is there anything wrong in the procedure? it
> >> seems
> >> > that the charges generated somehow related to the sequence of the
> >> concatenate
> >> > esp files.....is it?
> >> >
> >> > or shall i just do resp calculation for separate 24 orientations and
> >> average
> >> > the charges generated?
> >> >
> >> > Pls advice......
> >> >
> >> > Thank you very much.
> >> >
> >> > Regards,
> >> > colvin
> >>
> >> http://q4md-forcefieldtools.org/FyD/
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Wed Jun 30 2010 - 02:00:03 PDT
