Dear Prof. Case,
I just used the same command with changing the output format from mol2 into
pdb and the charges I got it from punch file.
antechamber -i isph_BS2_ESP.log -fi gout -o isph_BS2_charges.pdb -fo pdb -c
resp -nc -3 -m 1 -j 0
I tried Antechamber from AmberTools 1.5 and AmberTools 12.
I am new user for AmberTools, may be I missed something.
Best regards,
Safwat
On Fri, Mar 15, 2013 at 3:13 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Mar 11, 2013, safwat abdel-azeim wrote:
>
> >I am calculating RESP charges using Antechamber of iron-sulfur cluster
> >complex. I used BS-DFT to optimize the geometry and UHF/6-31G* to
> >calculate ESP with the same wave function. But when I used antechamber
> >to get RESP charges using the following commands, it gave totally
> >different charges, for ex. for Phosphorus it changes from positive to
> >negative. I used g03 to generate ESP and Amber12. Can you help me to
> >figure out this error. Why when I used Mol2 and PDB output file
> >format the results are different.
> >
> >Case-1- antechamber -i isph_BS2_ESP.log -fi gout -o
> >isph_BS2_charges.mol2 -fo mol2 -c resp -nc -3 -m 1 -j 0
> >
> >Case-2- antechamber -i isph_BS2_ESP.log -fi gout -o
> >isph_BS2_charges.pdb -fo pdb -c resp -nc -3 -m 1 -j 0
>
> I am confused here. The pdb output file from antechamber doesn't include
> charges. Can you say exactly how you are getting the charges in Case-2?
>
> You should also give information about which version of antechamber you are
> using.
>
> ...thx..dac
>
>
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>
--
-----------------------------------------------------------
Safwat Abdel-Azeim, PhD
Computational Chemistry (Modeling of Biomolecules)
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Received on Fri Mar 15 2013 - 06:00:04 PDT
