AMBER Archive (2009)

Subject: Re: [AMBER] failure to run antechamber with amber 10

From: George Tzotzos (gtzotzos_at_mac.com)
Date: Thu Jan 29 2009 - 16:48:50 CST

Hi Francesco,

I observed the same problem and posted several mails (see thread: Re:
[AMBER] Antechamber ligand prep) (January 27, '09). If you try instead
of myfile.pdb, myfile.mol2 (dac's suggestion) you may find it that it
works. I'm not terribly happy with this solution, so if you find an
answer to the problem please post.

All the best

George
On Jan 29, 2009, at 11:29 PM, Francesco Pietra wrote:

> hi:
>
> with amber10/ambertools 1.2 i was unable to run antechamber, as
> indicated below (i can't remember if this is the 1st time i am dealing
> with antechamber in ambertools 1.2)
>
>
>
> $AMBERHOME/exe/antechamber -i myfile.pdb -fi pdb -o myfile.prepin -fo
> prepi -c bcc -s 2
>
> returned the error:
>
> Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
> Running: /usr/local/amber10/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> ===
> with amber 9 - installed in the same machine - the above procedure
> (without retyping) could be carried out correctly.
>
> thanks for detecting the origin of the problem
>
> francesco pietra
>
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