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Original Post (Thread Starter)
#34968 05/07/2015 6:38 PM
by talbers
I'd like to run MD on a protein that has an SAM (S-adenosyl methionine) ligand. The question has come up before (here: and people mentioned that there was a patch somewhere.

In CHARMM36 this patch SAM seems to have disappeared, at least I can't find it anywhere, and cationic tricoordinate sulphur isn't parametrized in cgenff or CHARMM. Does anyone have a topology and parameters?

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#38362 Oct 17th a 04:15 PM
by rmv
This is appears to be more of a basic usage issue, and not a parameter issue. Many of the errors arise from initial attempt to read coordinates from a PDB file, which is NOT a native CHARMM format; it can be used for import, but often requires extra steps, esp. if there are any residues missing coordinates. Another issue is the use of BOMLEV -19, which is extreme, and ill-considered.

Suggested reading from the Script Archive: complex PDB input examples
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#38363 Oct 17th a 08:12 PM
by rmv
There is a parameter error of sorts, in that you've only read the protein topology and parameter files. From the comments in the file toppar_all36_prot_na_combined.str:

!Parent files that have to be read prior to streaming this file

Also, creating your own custom topology and parameter files by combining existing distributed files is not recommended for the general user. It is best to read them from a standard location, and not change those files in any way
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