On Tue, Nov 6, 2012 at 3:30 PM, Yulin Huang <yulinhuang2007.gmail.com>wrote:
> Dear Professor:
> Thank you very much for your reply.
> I have two ligands with identical atom names and orders for the
> corresponding same atoms. I place the different atom at the end of mol2
> files. After I ran Antechamber as the follows,then prep files with
> different orders for corresponding same atoms were generated.
>
> antechamber -i *.lig.mol2 -fi mol2 -o *.lig.ante.pdb -fo pdb
> antechamber -i *.lig.mol2 -fi mol2 -o *.lig.ante.prep -fo prepi
> parmchk -i *.lig.ante.prep -f prepi -o *.lig.ante.frcmod
>
> Then the parm files and coordinates with different orders were also
> generated after this. TI cannot work.
>
What Dave suggested was do not use the prep file format _at all_. Just use
mol2. With the exception of some connection information (specifically, the
atoms that bond with adjacent residues), the information in both file
formats is exactly the same.
Another possibility is to use -prepc instead of -prepi (which I would
assume has less of a reason to re-order atoms).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 06 2012 - 14:30:03 PST
