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

From: Bruno Falcone <>
Date: Tue, 13 Dec 2016 11:33:25 -0300

Hi, sorry to jump in the conversation but hope I can be of any use.

The problem I can see is that you set the charge to be 0 whereas it is
+1 since you have a protonated nitrogen in the aliphatic ring.

I ran antechamber with the +1 charge and I obtained the structure attached.



On 13/12/16 11:14, Andreas Tosstorff wrote:
> 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

AMBER mailing list

Received on Tue Dec 13 2016 - 07:00:02 PST
Custom Search