Water and cofactors minimisation

[Miro]

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

[David Koes]

No, you can only minimize/dock a single discrete molecule at a time. Perhaps you should look into using a molecular dynamics code?

David Koes

Assistant Professor
Computational & Systems Biology
University of Pittsburgh

On Dec 24, 2018, at 5:19 AM, Miro mirix@users.sourceforge.netamp#109;amp#105;amp#114;amp#105;amp#120;amp#64;amp#117;amp#115;amp#101;amp#114;amp#115;amp#46;amp#115;amp#111;amp#117;amp#114;amp#99;amp#101;amp#102;amp#111;amp#114;amp#103;amp#101;amp#46;amp#110;amp#101;amp#116; wrote:

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

---

Water and cofactors minimisationhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fsmina%2Fdiscussion%2Fhelp%2Fthread%2F26e121f1bf%2F%3Flimit%3D25%231a4c&data=02%7C01%7Cdkoes%40pitt.edu%7C35b7d8b47785486f202f08d66989455a%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636812435638881385&sdata=Si0BM2s1nl93acDf8WD6TRi4jrsaabrhNdhGTF212hI%3D&reserved=0

---

Sent from sourceforge.nethttp://sourceforge.net because dkoes@pitt.edudkoes@pitt.edu is subscribed to https://sourceforge.net/p/smina/discussion/help/https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fsmina%2Fdiscussion%2Fhelp%2F&data=02%7C01%7Cdkoes%40pitt.edu%7C35b7d8b47785486f202f08d66989455a%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636812435638881385&sdata=3K2vIO1IfLtJwvlvxkjzLxIRAmckgyMWaFDDs0ripdQ%3D&reserved=0

To unsubscribe from further messages, a project admin can change settings at https://sourceforge.net/p/smina/admin/discussion/forums.https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fsmina%2Fadmin%2Fdiscussion%2Fforums.&data=02%7C01%7Cdkoes%40pitt.edu%7C35b7d8b47785486f202f08d66989455a%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636812435638891394&sdata=J9SOCxK1bf%2FJcK9NHk%2BY0sZc55r95Gjv5aYWHtgQZhc%3D&reserved=0 Or, if this is a mailing list, you can unsubscribe from the mailing list.

[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.