Hi Divya,
Can you send your input files to my email address (ambermailpengfei@gmail.com <mailto:ambermailpengfei@gmail.com>, please see the "Question” section in the tutorial
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> before you send the email)? I can help to do a check.
-Pengfei
> On Jul 31, 2019, at 8:09 AM, Divya Rai <drai550.gmail.com> wrote:
>
> I have been following the AMBER tutorial on MCPB.py. Everything was going
> smooth until the step:
>
> * MCPB.py -i 1OKL.in -s 2 *
>
> My system comprises of a Zinc metal bounded to 3 His residues and 2 water
> molecules. While using the above command, the following error shows:
>
>
>
>
>
>
>
>
>
> *==================Using the Seminario method to solve the
> problem.Traceback (most recent call last): File
> "/home/st/amber14/bin/MCPB.py", line 434, in <module> g0x) File
> "/home/st/amber14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py",
> line 309, in gene_by_QM_fitting_sem 'Force Field') File
> "/home/st/amber14/lib/python2.7/site-packages/pymsmtmol/gauio.py", line 43,
> in get_crds_from_fchk if (i > beginl) and (i < endl):UnboundLocalError:
> local variable 'beginl' referenced before assignment*
>
> So, I tried using the Empirical method (* MCPB.py -i 1OKL.in -s 2e*)
> instead which worked quite well. However, since then I am unable to
> calculate the RESP charges using MCPB.py. I even used the script in order
> to overcome the bug as mentioned in your tutorial. But the final result of
> the script is showing the same error which was shown before when I use the
> command :
> *MCPB.py -i 1OKL.in -s 2 *
>
> And the error is:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ****Generating the 1st stage resp charge fitting input file...***Generating
> the 2nd stage resp charge fitting input file...***Doing the RESP charge
> fiting...sh: 1: espgen: not foundsh: 1: resp: not foundsh: 1: resp: not
> foundTraceback (most recent call last): File
> "/home/st/amber14/bin/MCPB.py", line 461, in <module> premol2fs,
> mcresname, 1, ionchgfix) File
> "/home/st/amber14/lib/python2.7/site-packages/mcpb/resp_fitting.py", line
> 453, in resp_fitting chgs = read_resp_file('resp2.chg') File
> "/home/st/amber14/lib/python2.7/site-packages/mcpb/resp_fitting.py", line
> 15, in read_resp_file fp = open(fname, 'r')IOError: [Errno 2] No such
> file or directory: 'resp2.chg'*
>
> Kindly help.
>
> I have been stuck since long.
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Received on Wed Aug 07 2019 - 20:00:02 PDT
