Re: [AMBER] MCPB Step 2s help

From: Tavenor, Nathan Albert <>
Date: Wed, 13 Jan 2016 12:49:47 +0000

Thanks for the response! I have been following that exact tutorial and tried using the same input as before, but received the error I posted.


From: Pengfei Li <>
Sent: Tuesday, January 12, 2016 12:16 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB Step 2s help

Hi Nathan,

> On Jan 11, 2016, at 3:30 PM, Tavenor, Nathan Albert <> wrote:
> 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/", line 441, in <module>
> gaff, frcmodfs, watermodel)
> File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/mcpb/", 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/", line 427, in get_parm_dict
> parmdict3 = read_frcmod_file(i)
> File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/pymsmtlib/", line 269, in read_frcmod_file
> dihparms = readdih(dihparms, line)
> File "/opt/sam/rhel6/amber/amber14.T15/lib/python2.7/site-packages/pymsmtlib/", 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 file. Can someone please help?

For all the steps of processing, there is only one input file needed. You can use the same input file as you used in the step 1. The only thing you need to change is use 2s after the -s option.

Here is a related tutorial about how to use to do the modeling: <>

You can check this tutorial for more information.

If you have questions, please feel free to email me.


> Thanks,
> Nathan
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Received on Wed Jan 13 2016 - 05:00:03 PST
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