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.
On Mon, Aug 31, 2009 at 1:08 PM, Barbault
Florent<florent.barbault.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.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.univ-paris-diderot.fr
>
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>
Received on Wed Sep 02 2009 - 23:06:37 PDT
