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
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >> _______________________________________________
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> >>
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Received on Thu Nov 03 2016 - 03:30:02 PDT
