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 Tue Jun 29 2010 - 23:30:04 PDT
