AMBER Archive (2009)

Subject: Re: [AMBER] How to derive charges from the output

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Aug 31 2009 - 15:35:46 CDT

Dear Florent & Bharat Lakhani,

> Actually my output contains Fe-Porphrin with cysteine residue. when i
> am runing this command it missing Fe as well as cysteine in the prein
> file. Here i am attaching my gaussian log file and prepin file also.
> Please let me know the proper way in order to calculate RESP fitting
> charges on metal ions.

Antechamber deals only with organic structures & is strongly connected
to GAFF.

Thus, you should try to use R.E.D. which handles metal complexes; FF
libraries generated by R.E.D. can be used in association with various
force fields. There were several emails in the q4md-fft mailing list
about metal complexes: I am sure you will find some of these emails
useful.

Finally, the prep.in force field libary format is more complex to
understand. My feeling is that the Tripos2 mol2 file format is more
intuitive and can be displayed in many graphical programs...

regards, Francois

> On Mon, Aug 31, 2009 at 1:08 PM, Barbault
> Florent<florent.barbault_at_univ-paris-diderot.fr> wrote:
>> Hello,
>>
>> I think there is a more simple way to do it. Personnaly, I use this command:
>>
>> antechamber -i gauss_output -fi gout -o prep.prepi -fo prepi -c resp -rn LIG
>>
>> Afterward, I reading the created file (prep.prepi) with an editor.
>> Last column
>> is the partial atomic charge derived with resp. You can also open this file
>> with xleap in order to localize each atom with their respective charge.
>>
>> I hope this will help you.
>> Regards,
>> Florent Barbault
>>
>> Le lundi 31 août 2009, bharat lakhani a écrit :
>>> Respected sir,
>>>                           I have GAUSSISN output log file. I want to
>>> derive the partial charges from this log file. I am running these
>>> following commands. Please suggest me.Is i am doing right or not. Its
>>> very urgent.
>>>
>>>
>>>
>>> antechamber -i DRUG.log -fi gout -o $line.ac -fo ac
>>> espgen -i DRUG.log -o $line.esp
>>> respgen -i DRUG.ac -o $line.respin1 -f resp1
>>> respgen -i DRUG.ac -o $line.respin2 -f resp2
>>> resp -O -i DRUG.respin1 -o $line.respout1 -e $line.esp -t qout_stage1
>>> resp -O -i DRUG.respin2 -o $line.respout2 -e $line.esp -q qout_stage1
>>> -t qout_stage2
>>> antechamber -i DRUG.ac -fi ac -o $line_resp.ac -fo ac -c rc -cf qout_stage2
>>> atomtype -i DRUG_resp.ac -o $line_resp_at.ac -f ac -p amber
>>> prepgen -i DRUG_resp_at.ac -o $line_int.prep -f int -rn SUS -rf SUS.res
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>>
>> -------------------------------------------------
>> Dr Florent Barbault
>> Maitre de conferences
>> Universite Paris Diderot
>> Laboratoire ITODYS
>> 15 rue Jean de Baïf, bâtiment Lavoisier
>> 75013 Paris FRANCE
>> http://www.itodys.univ-paris7.fr/spip.php?article77
>> tel  : (33) 01-57-27-88-50
>> e-mail : florent.barbault_at_univ-paris-diderot.fr

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