AMBER Archive (2006)

Subject: Re: AMBER: RESP charges of iron-porphyrin system

From: Shin Tokumoto (stokumoto_at_tara.tsukuba.ac.jp)
Date: Thu Oct 19 2006 - 23:45:08 CDT

Dear Seabra,

Thank you very much for your kindly suggestion.

Actually I did in the same way as you mentioned before. Namely, I added
the following sentence to the
Gaussian Input, performed the Gaussian, and then got the log file:

#p uhf/6-31+g geom=conenctivity density=checkpoint pop=(mk,readradii)
iop(6/33=2,6/42=6)

But, as I said before, the antechamber did not work well if I used this
output as the antechamber input.

Let me say what I did to perform the antechamber. Using the above
Gaussian output, I performed the antechamber
for the iron-porphyrin system with the following command.

$ AMBERHOME/exe/antechamber -i myfile.log -fi gout -o myfile.prep -fo
prepi -c resp -nc total_charge -m spin_multiplicity

After that, I could get the prep file, but in the file there was no
information about the iron RESP charge.

Am I right in performing the antechamber correctly? I have already
succeeded in getting the RESP charge for the non-iron
system, i.e., only porphyrin ring, by following the above steps. But in
this iron system I did not.

Would you please give me any advice about this?

Shin Tokumoto

Gustavo Seabra wrote:
> To get Gaussian to generate the RESP charges you can use a route card
> like:
>
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6)
>
> The HF/6-31G* is the standard method for generating RESP charges for
> GAFF parameters, SCF=tight is always recommended, and Test just tells
> Gaussian not to bother with job archiving.
>
> The really important keyword here is Pop=MK, which tells Gaussian to
> "Produce charges fit to the electrostatic potential at points selected
> according to the Merz-Singh-Kollman scheme" [quote from G03 manual].
> IOp(6/42=6) tells it to use 6 points per unit area in the RESP fit.
> [IOp(6/33) is not documented, so I can't tell much without having
> access to G03 source code.]
>
> By the way, that's what you would get if you just used antechamber to
> create the G03 input file:
>
> $ antechamber -fi pdb -i myfile.pdb -fo gcrt -o myfile.com
>
> Or something like it, depending on the kind of files you have.
>
> HTH,
>
> Gustavo Seabra.
>
>
> On 10/18/06, Shin Tokumoto <stokumoto_at_tara.tsukuba.ac.jp> wrote:
>> Dear Amber users,
>>
>> Regarding RESP charge of Fe, I have a question.
>>
>> I would like to calculate RESP charges of iron-porphyrin system.
>> First I performed Gaussian03 on this iron-porphyrin system, adding to
>> the input
>> file both a keyword, "pop=readradii", and the value of Fe V.D.W radius
>> to get the
>> electrostatic potential. By using the output file, I then performed
>> antechamber and
>> could get a prep file. But there was no information about the Fe RESP
>> charge in this file,
>> that is to say, the corresponding place is empty.
>>
>> Would you tell me how to get the correct RESP charge of Fe?
>>
>> Thanks for any help.
>>
>> Shin tokumoto.
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