Hi Mahmood,
The bug has been fixed. Please go to: https://github.com/Amber-MD/pymsmt/find/release2 <https://github.com/Amber-MD/pymsmt/find/release2> to save the "msmtmol/gmsio.py" file as “gmsio.py” and use it to overwrite the gmsio.py file under $AMBERHOME/AmberTools/src/pymsmt/msmtmol/ directory, and reinstall the pyMSMT program by doing “cd $AMBERHOME/AmberTools/src/pymsmt/ && make install”, and then try to run the charge fitting step again. Please let me whether it works.
Kind regards,
Pengfei
> On Oct 28, 2016, at 3:25 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
> Hi Mahmood,
>
> There may be a bug there. You can send your large model MK calculation log file to my email address. I can help to do a check.
>
> Kind regards,
> Pengfei
>
>> On Oct 28, 2016, at 1:21 PM, Mahmood Jasim <ddfd09.gmail.com> wrote:
>>
>> Hi Amber users,
>>
>> I have been trying to use MCPB.py to parameterise the coordinate of a
>> protein containing 2 zinc ions. I am using GAMESS for optimization, force
>> constant and electrostatic potential calculations. I managed to run the
>> first step of MCPB.py and get the input files for GAMESS. GAMESS
>> calculations were finished with the required log files
>> (group_small_opt.log, group_small_fc.log, group_large_mk.log) and all the
>> calculations finished normally. The second step of MCPB.py also was done OK
>> but when trying to run the third step for charge fitting, I started to have
>> problems. The main error message I am getting is this:
>>
>> ******************************************************************
>> * *
>> *======================RESP Charge fitting=======================*
>> * *
>> ******************************************************************
>> ***Generating the 1st stage resp charge fitting input file...
>> ***Generating the 2nd stage resp charge fitting input file...
>> ***Doing the RESP charge fiting...
>> Traceback (most recent call last):
>> File "/apps/amber16/bin/MCPB.py", line 600, in <module>
>> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
>> File "/apps/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py",
>> line 443, in resp_fitting
>> get_esp_from_gms(mklogf, espf)
>> File "/apps/amber16/lib/python2.7/site-packages/msmtmol/gmsio.py", line
>> 222, in get_esp_from_gms
>> for i in range(bln, eln+1):
>> UnboundLocalError: local variable 'eln' referenced before assignment
>>
>>
>> It just generates RESP input files and then quits.
>>
>> Any advice please?
>>
>> Regards,
>> Mahmood Jasim
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Oct 29 2016 - 21:00:02 PDT
