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.html and
> > 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/
>
>
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Received on Wed Jun 30 2010 - 00:00:05 PDT
