Hi Mahmood,
You are welcome. Good to know that. Wish your research is going well!
Kind regards,
Pengfei
> On Nov 3, 2016, at 5:02 AM, Mahmood Jasim <ddfd09.gmail.com> wrote:
>
> Hi Pengfei,
>
> Yes the new code has worked for us in fitting the charges using GAMESS log
> files from 2 versions of GAMESS, so it is compatible with different
> versions of GAMESS
>
> Many thanks for your help.
>
> Regards,
> Mahmood
>
> On 1 November 2016 at 00:46, Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
>> Hi Mahmood,
>>
>> I am not sure whether it is because of the version problem. When I wrote
>> the original code, I just used one version as reference.
>>
>> Glad to know that it works. I think the code now is compatible with
>> different versions.
>>
>> Kind regards,
>> Pengfei
>>
>>> On Oct 31, 2016, at 11:21 AM, Mahmood Jasim <ddfd09.gmail.com> wrote:
>>>
>>> Hi Pengfei,
>>>
>>> We ran the large model MK calculation using a newer version of GAMESS for
>>> Windows that operate on 64-bit system and ended with the same error
>> message
>>> when we tried the third step of MCPB.py. After that we applied the bug
>> fix
>>> you suggested and everything was working just fine; mol2 files for the
>>> coordination site were generated with charges on the individual atoms. We
>>> went on with the 4th step and using tleap to get the prmtop and inpcrd
>>> files. We viewd the files with VMD and all seems great.
>>>
>>> Thank you very much for your help.
>>>
>>> Regards,
>>> Mahmood Jasim
>>>
>>> On 30 October 2016 at 03:33, Pengfei Li <ambermailpengfei.gmail.com>
>> wrote:
>>>
>>>> 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 Tue Nov 08 2016 - 11:00:02 PST
