Hi everyone,
I am having trouble in parameterizing CO-METHYLCOBALAMIN (
https://www3.rcsb.org/ligand/cob) with MCPB.py.
I am able to generate comp_small_opt.com and comp_small_fc.com but
standard model fails.
I am attaching the files i used to generate the parameters and initial
start files for your reference.
******************************************************************
* *
*=======================Building models==========================*
* *
******************************************************************
***Creating the small model...
It contains the residue 1-COB as normal.
Totally there are 182 atoms in the small model.
Totally there are 687 electrons in the small model.
***Creating the standard model...
It contains the residue 1-COB as normal.
Traceback (most recent call last):
File "/home/abhilash/amber16/bin/MCPB.py", line 562, in <module>
premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
File
"/home/abhilash/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 1742, in gene_model_files
bdedatms, libdict, autoattyp)
File
"/home/abhilash/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 1319, in build_standard_model
attype = libdict[resname + '-' + atname][0]
*KeyError: 'COB-CO*'
Regards
Abhilash
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: CO.mol2
- application/octet-stream attachment: COB.mol2
- application/octet-stream attachment: comp.in
- chemical/x-pdb attachment: CO.pdb
Received on Wed Mar 08 2017 - 02:00:03 PST
