Re: [AMBER] converting amber files

From: mohammad r <>
Date: Tue, 18 Aug 2015 13:49:37 +0000 (UTC)

Thank you for your help;Sorry to ask my question here, I couldn't find any other website corresponding to acpype or mailing list and as I want to convert amber files, I thought that it's better to ask my question here.I typed the "$PWD/acpype" then it said that it is a directory. but still the acpype doesn't work.
and in the link:, in the section "To Test" as I type the command "../ -i FFF.pdb", I get the error:================================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2014-08-27 18:33:08Z Rev: 7828 (c) 2015 AWSdS |
ERROR: no 'babel' executable; you need it if input is PDB
ERROR: otherwise use only MOL2 or MDL file as input ... aborting!
Total time of execution: less than a second

Thank you again.

     On Tuesday, August 18, 2015 5:57 PM, Jason Swails <> wrote:

 On Tue, Aug 18, 2015 at 9:10 AM, mohammad r <>

> Thank you George;I've done the procedure mentioned in the website.
> I've downloaded the acpype with "svn checkout
> acpype" command. but when I
> installed it with "sudo ln -s $PWD/ /usr/local/bin/acpype"
> command. but when I try to use "acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd"
> command, the error appeared .

​You have to make sure that $PWD/acpype is executable.

That said, you should be consulting the acpype user's forum or mailing list
for help with acpype -- *not* the Amber list.  It is unlikely many people
that respond regularly on this list use acpype on a regular basis (or at

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 18 2015 - 07:00:06 PDT
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