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.
I am wondering are there any tutorials for TI for small molecules
setups(the real molecules with larger transformations, different rings,etc)
in AMBER 11 or AMBER12 ? Based on my experience, ligand pairs with simply
different atoms at the same position (C to N) can work. But ligand pairs
with larger transformation (ethyl to methyl ) cannot work, for antechamber
rearranges the order of the atoms. In addition, manually modifying the
corresponding atom names to be identical takes too long and is prone to
errors. Many thanks.
On Tue, Nov 6, 2012 at 3:06 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Nov 06, 2012, Yulin Huang wrote:
>
> > Thanks everyone for the help. I tried many methods, but I realize I have
> > to have prep files in the same order for TI. Even I built the mol2, pdb
> > files with the same order for corresponding atoms, I still have different
> > prep files which cause the problem. Does anyone has the experience of
> > mapping one prep file to the other one with the same atoms in the order?
>
> Don't use prep files(?) I would love to finally retire this format. Does
> the
> same problem appear if you use mol2 instead?
>
> ...dac
>
>
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--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Tue Nov 06 2012 - 13:00:03 PST
