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. See: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#antechamber> I hope this helps, Elaine ----- 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@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