[AMBER] MCPB Step 2s help

From: Tavenor, Nathan Albert <nat24.pitt.edu>
Date: Mon, 11 Jan 2016 20:30:42 +0000

Hello all,

I'm currently trying to paramaterize a non-natural residue as a metal ligand complex. I'm trying to use the Seminario method to generate the forcefield parameters from the force constants generated by Gaussian, but keep getting the following error:
Traceback (most recent call last):
  File "/opt/sam/rhel6/amber/amber14.T15/bin/MCPB.py", line 441, in <module>
    gaff, frcmodfs, watermodel)
  File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/mcpb/gene_pre_frcmod_file.py", line 37, in gene_pre_frcmod_file
    Params = get_parm_dict(ffchoice, gaff, frcmodfs)
  File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/pymsmtlib/lib.py", line 427, in get_parm_dict
    parmdict3 = read_frcmod_file(i)
  File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/pymsmtlib/lib.py", line 269, in read_frcmod_file
    dihparms = readdih(dihparms, line)
  File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/pymsmtlib/lib.py", line 157, in readdih
    has_pero = [abs(int(i.strip().strip('.'))) for i in has_pero]
ValueError: invalid literal for int() with base 10: '-1.0'

I've converted the final Gaussian .chk file from the Freq calculation to .fchk format. It's unclear to me what the required input files for this step are or what all should be included in the input.in file. Can someone please help?


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Received on Mon Jan 11 2016 - 13:00:04 PST
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