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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>>>
>>
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Received on Mon Oct 31 2016 - 18:00:02 PDT
