> Somebody treat the bond between the SG of CYM and the
> ZN as a covalent bond. I have tried this way, the
> situation is that the prepin file of the CYM-ZN.pdb
> lackes the information of the ZN and the last two
> atoms (I think the last 2 atoms should be ZN), thus in
> the frcmod file, there is no information on the ZN
> related bonds.
ZN is not an organic molecule, so creating the necessary force field
parameters is not that easy. If someone has already created those
parameters for ZN, use those parameters.
> The other question is about the command you mentioned:
>
>
> antechamber -i CYM.pdb -fi pdb -o cym.in -fo gcrt
This command will create a gaussian input file, which u will run using
gaussian. After getting the gaussian output file, u can use antechamber
-again- to get the resp charges.
One other thing is that, there is already a CYM residue defined in the
amber force field; so u dont need to do anything. As I wrote in my prev.
email, I assumed that u are trying to get the resp charges for this
particular molecule. As CYM residue is already defined in the force field,
I dont think that u need to do any gaussian calculation and get the resp
charges.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Nov 29 2006 - 06:07:09 PST
