[Chimera-users] Minimization with sulfur atom

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 30 08:49:16 PDT 2019

Hi Sara,
The Antechamber program (part of Ambertools, included with Chimera) is called to calculate parameters for “nonstandard” residues like most ligands.  It handles a variety of organic molecules, but not everything: it may fail on certain types, like those with high charge density.  In that case, there is nothing we can say except to try using the simpler charge calculation method, Gasteiger, instead of AM1-BCC.


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 30, 2019, at 12:10 AM, sara20 at mail.ustc.edu.cn wrote:
> Dear users
> I have complex structure with ligand having sulfur atom in it. I am trying to minimize it but it fails giving the following error:
> (LIG) /home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/antechamber: Fatal Error!
> (LIG) Cannot properly run "/home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/sqm -O -i sqm.in -o sqm.out".
> I assume it's because of sulfur atom in ligand because I tried running it with out sulfur and it worked fine.
> I checked  MMKT Atom database for sulfur file and it's already there:
> name = 'sulphur'
> symbol = 'S'
> mass = [(31.97207070, 95.02), (32.97145843, 0.75),
>         (33.96786665, 4.21), (35.9670806, 0.02)]
> color = 'yellow'
> vdW_radius = 0.18
> b_coherent = 2.847*fm
> b_incoherent = 0.188*fm
> b_coherent_deut = 2.847*fm
> b_incoherent_deut = 0.188*fm
> Any help would be highly appreciated. Thanks
> Sara

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