Hi, Dr. Pengfei Li and Amber users,
I am currently trying to create topology (prmtop) and coordinate (inpcrd)
for a small molecule *OCTAHEDRAL RU-PYRIDOCARBAZOLE* (FLL) of PDB id*
3FXZ. *I followed the Amber tutorial
*
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
<
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>*
but Generate the PDB, Gaussian, GAMESS-US and fingerprint modeling files
with the command line
*MCPB.py -i FLL.in -s 1*
there is a key error
***Creating the small model...
It contains the residue 1-FLL as normal.
Totally there are 62 atoms in the small model.
Traceback (most recent call last):
File "/home/fulbabu/program/amber16/bin/MCPB.py", line 644, in <module>
addred, lgchg, lgspin)
File
"/home/fulbabu/program/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
line 1895, in gene_model_files
smspin, addred, outf, sqmopt)
File
"/home/fulbabu/program/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py",
line 1380, in build_small_model
AtNum = Atnum[gatm.element]
KeyError: 'R'
I couldn't understand how to fix it?
My all files are attached below,
***************
Kind regards
*Md Fulbabu Sk*
*Ph.D. Research ScholarDiscipline of BioSciences and Biomedical Engineering
(BSBE)Indian Institute of Technology Indore (IITI), India*
Computational BioPhysics Group IITI (Kar's Lab)
<
https://iitibsbeparimalkar.wixsite.com/biophysics>
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- chemical/x-mol2 attachment: RU.mol2
- application/octet-stream attachment: FLL.in
Received on Wed Feb 06 2019 - 02:00:02 PST
