[gmx-users] Ligand charge issues

Alan alanwilter at gmail.com
Mon Sep 2 12:47:47 CEST 2013

In https://code.google.com/p/acpype/ you can look the wikis and you see the
explanations about the partial charges.

The best solution, though not straightforward, would be using


On 2 September 2013 11:27, Muhammad Ayaz Anwar <ayazanwar at hotmail.com>wrote:

> Hi Gromacs users,
> I am studying the protein-ligand interaction using amber99sb-ILDN force
> field in gromacs 4.6.2. To create the ligand topology (lipid A), I have
> used online version of ACPYPE/antechamber.
> http://webapps.ccpn.ac.uk/acpype/
> I have read a lot more time that charge on different atoms are not correct
> when created through various softwares/scripts. My question is whether
> ACPYPE/antechamber also fall in this category? If yes, can anyone please
> provide me with any link from where I can get charge values to assign?
> Thank you.mayaz
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

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