On Sun, Dec 21, 2014 at 11:36 AM, Yaser Hosseini <yaser790.yahoo.com> wrote:
>
> i install amber and amber tools but when i want run this command i get
> some error:
> acpype -i ref-ligandChimera.mol2 -c user
> acpype -i ref-ligandChimera.mol2 -c user
>
> ================================================================================================
> | ACPYPE: AnteChamber PYthon Parser interfacE v. 2014-08-27 18:33:08Z Rev:
> 7828 (c) 2014 AWSdS |
>
> ================================================================================================
> WARNING: no 'babel' executable, no PDB file as input can be used!
> ==> Reading user's charges from mol2 file...
> ==> ... charge set to 0
> ==> Executing Antechamber...
> ==> AC output file present... doing nothing
> ==> * Antechamber OK *
>
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: 1: -i: not found
>
I'm not familiar with acpype. But if I had to guess, I would say this
error message suggests that parmchk is not currently installed. The error
message says that the command "-i" cannot be found, and my guess is that
parmchk is being executed something like:
$parmchk -i <input_file> -o <output_file> ...
and since parmchk can't be found, that item is blank and the shell tries to
execute "-i", which doesn't exist. parmchk *should* be installed as part
of AmberTools. If it is not, then you have not installed Amber correctly
and you need to go back and do it again.
You will need the following programs in order to run acpype (I believe):
antechamber, parmchk, and tleap. If those programs aren't *all* in
$AMBERHOME/bin, then acpype will fail. If you install AmberTools 14
correctly, all three of those programs should be present.
As an aside to the acpype developer(s) (if they monitor this list) -- I
suggest replacing "parmchk" with "parmchk2", which does a better job
matching the "best" parameters in gaff.dat with the atom types from your
molecule.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 21 2014 - 11:30:02 PST
