[AMBER] Creating PRMTOP and INPCRD in Amber 16

From: Fulbabu Sk <phd1701171005.iiti.ac.in>
Date: Wed, 6 Feb 2019 15:00:55 +0530

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

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)
line 1895, in gene_model_files
    smspin, addred, outf, sqmopt)
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)

AMBER mailing list

Received on Wed Feb 06 2019 - 02:00:02 PST
Custom Search