Re: [AMBER] force field parameter and resp charge calculation

From: FyD <>
Date: Tue, 29 Jun 2010 18:27:08 +0200

Dear Colvin,

You might look at R.E.D. III.3 as well where multiple orientation
and/or multiple conformation charge fit can be automatically carried
out. You might look at our tutorial as well:
However, it has just been updated for R.E.D.-III.4, which will be
released soon.

With R.E.D. IV June 2010 in R.E.D. Server 2.0, we will also release a
new statistics module, which allows automatic charge value comparisons
between conformation/orientation, fitted versus (vs) averaged charges,
Mulliken/Lowdin vs MEP-based charges, multiple molecule charge fit vs
single molecule charge fit, with charge constraint vs without charge
constraint during charge fitting, etc...

MEP-based charge values generated by R.E.D./R.E.D. server &
Antechamber should be identical if the same orientations/conformations
are used. Thus, you could use results obtained with one program to
check what is obtained with the other one...

Finally, when you manually concatenate RESP espot files for
Antechamber (R.E.D. does that automatically), just be sure you do not
have empty lines at the end of each espot files; otherwise this will
mess up your multiple orientation/conformation RESP fit (in the
multiple espot file).

regards, Francois

Quoting colvin <>:

> 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 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 -fi ac -o -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 (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 (same apply
> to 24-21molecules, 24-15molecules and 24-1 molecules, the charges are the
> same --> charge set C)
> I am confuse with there anything wrong in the procedure? it seems
> that the charges generated somehow related to the sequence of the concatenate
> esp 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 - 09:30:03 PDT
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