Miro

Thanks. I am currently using UCSF Chimera, which is fair enough but slow. The problem with other options is parametrisation. When I'll have the time I might give OpenMM/Smirnoff a go.

Thanks. I am currently using UCSF Chimera. When I'll have the time I might give OpenMM/Smirnoff a go.

Is it possible to minimise water and cofactors along with the ligand and the binding site residues? I have tried including them as part of the receptor (both as ATOM and as HETATM, respectively) and verified that they are in input pdbqt, however they are not in the output file. If, on the other hand, I include them as part of the ligand pdbqt file, smina complains about a formatting issue with the input file and refuses to run. Best, Miro

Confirmed. Compiling with the OB development version solves the issue.

Yes, it does. So you are using the OpenBabel development version 2.3.90, right?

Hmm. It is the stable release 2.3.2 installed via the package manager in Ubuntu 14.04......

No, I compiled it from source (git) last week. I will try the precompiled versio...

No, I compiled it from source last week. I will try the precompiled version.