Dear Prof. Case,
I have used the following command in amber11 i.e. am1bcc in amber11 and bcc
in amber10.
But command with bcc is not successful due to convergence failure in
amber11.
The generated prep file is attached for your kind reference.
Command in amber11
--------
[vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69_1.prep -fo
prepi -c am1bcc -s 2
Running: /opt/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /opt/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Running: /opt/amber11/bin/prepgen -i ANTECHAMBER_PREP.AC -f int -o
VD69_1.prep -rn "UNN" -rf molecule.res
[vaibhav.localhost VD69]$
------
On Thu, Aug 25, 2011 at 7:46 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Aug 25, 2011, vaibhav dixit wrote:
> >
> > But the same set of commands for this ligand (VD69) gave the following
> error
> > in amber11. (This error did not appear when I used am1bcc in place of bcc
> in
> > amber11)
>
> I am still confused: can you say *exactly* what you did you when you "used
> am1bcc in place of bcc in amber11"? This may help us to track down the
> problem.
>
> See also Dan Roe's reply as well.
>
> ...thanks!...dave case
>
>
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Thu Aug 25 2011 - 23:00:02 PDT
