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frchalaoux / acpype

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Ligand parametrization: charged species not recognised #9

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Following the tutorial "How To Use NAMD with AMBER Output Topologies From 
ACPYPE"
2. Using acetyl salicylate as ligand.

What is the expected output? What do you see instead?

Antechamber fails because acpype reports the charge of the ligand as being 0, 
but it is -1. Therefore the number of electrons is wrong.

The problem happens both with the ligand in PDB format and with the ligand in 
MOL2 format with AM1-BCC charges.

What version of the product are you using? On what operating system?

SVN trunk as per Wednesday June 06 at 8:00.

Debian 7 64-bit. 

Please provide any additional information below.

Original issue reported on code.google.com by miromo...@gmail.com on 6 Jun 2012 at 7:01

GoogleCodeExporter commented 8 years ago 
The "guess charge" routine is not perfect and it'll never be. Use the option 
`-n` to set the charge value. You should know about your molecule.

Original comment by alanwil...@gmail.com on 22 Jul 2013 at 12:44

GoogleCodeExporter commented 8 years ago 
"You should know about your molecule." 

I have millions, so, no, unfortunately, I can not know all of them. 

In fact, I was looking for an automatic procedure, knowing it can not be 
perfect.

I ended up using UCSF Chimera in batch mode in order to assign the total 
charge. I guess it is not perfect either, but it has worked flawlessly so far 
(even with not-so-frequent functional groups containing S, P, Se, etc...

Original comment by miromo...@gmail.com on 22 Jul 2013 at 12:50