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MJ@SPPU
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Original Post (Thread Starter)
#34968 05/07/2015 6:38 PM
by talbers
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: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1980) 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?

Thanks
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#38362 Oct 17th a 04:15 PM
by rmv
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
1 member likes this
#38363 Oct 17th a 08:12 PM
by rmv
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
!top_all36_prot.rtf
!par_all36_prot.prm
!top_all36_na.rtf
!par_all36_na.prm


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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