[AMBER] MCPB.py error in Step 2

From: Jon Mujika <joni.mujika.ehu.es>
Date: Thu, 10 Nov 2016 12:25:11 +0100

Dear Amber users,

I am trying to get parameters for Ti(IV) and its protein binding site using
MCPB.py, as implemented in AmberTools16. I followed the Tutorial kindly
provided by Pengfei Li. I managed to generate all the files (fingerprint
files, G09 inputs, …) and afterwards I run the G09 calculations. However,
when I try to get the force field parameters (MCPB.py -i input.in -s 2) I
get the next error:


*===================Generate the Initial frcmod file=========***


Traceback (most recent call last):

File "/home/joni/Programs/amber16/bin/MCPB.py", line 575, in <module>

ff_choice, gaff, frcmodfs, watermodel)

File "/home/joni/Programs/amber16/lib/python2.7/site-packages/mcpb/gene_pre_frcmod_file.py",
line 54, in gene_pre_frcmod_file

Params = get_parm_dict(ffchoice, gaff, frcmodfs)

File "/home/joni/Programs/amber16/lib/python2.7/site-packages/lib/lib.py",
line 528, in get_parm_dict

parmdict3 = read_frcmod_file(i)

File "/home/joni/Programs/amber16/lib/python2.7/site-packages/lib/lib.py",
line 446, in read_frcmod_file

lndict[lnlist1[-1]] = (lnlist2[-1]+1, tln)

IndexError: list index out of range

I would appreciate any help solving the problem. I tried to attach the
files, but the attachment's size was to large.

Many thanks,

*Jon Iñaki Mujika*
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Received on Thu Nov 10 2016 - 03:30:03 PST
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