Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence

From: David A Case <>
Date: Tue, 13 Dec 2016 09:07:10 -0500

On Tue, Dec 13, 2016, Andreas Tosstorff wrote:
> I am running Ambertools16 on CentOS. I am not sure on the compiler,
> since I run this on a remote system and I did not install Amber myself
> myself.

What is the *exact* command line you used? This is what is needed:

antechamber -i <pdbfile> -fi pdb -o <mol2file> -fo mol2

Also: do the antechamber tests pass? The most likely explanation I can see is
that you are not really calling antechamber or acdoctor correctly, or that you
are giving it an empty or corrupted PDB file. Have you run antechamber on
other inputs?


AMBER mailing list
Received on Tue Dec 13 2016 - 06:30:03 PST
Custom Search