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
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Received on Tue Jun 29 2010 - 04:30:03 PDT
