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

From: Andreas Tosstorff <>
Date: Tue, 13 Dec 2016 15:14:12 +0100

Hi David,

this is the command line and output:

antechamber -i L01.pdb -fi pdb -o L01.mol2 -fo mol2 -c bcc
Total number of electrons: 195; net charge: 0
INFO: Number of electrons is odd: 195
       Please check the total charge (-nc flag) and spin multiplicity
(-m flag)

Running: /share/apps/amber16/bin/sqm -O -i -o sqm.out
Error: cannot run "/share/apps/amber16/bin/sqm -O -i -o sqm.out"
of bcc() in charge.c properly, exit

It works fine when not using the -c flag:

antechamber -i L01.pdb -fi pdb -o L01.mol2 -fo mol2

On 12/13/2016 03:07 PM, David A Case wrote:
> 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?
> ....dac
> _______________________________________________
> AMBER mailing list

M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
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Received on Tue Dec 13 2016 - 06:30:03 PST
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