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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Received on Mon Oct 31 2016 - 09:30:02 PDT
