Hi Pengfei,
Thanks for reply. Yes, both have the same atom and residue name in mol2 and
pdb files. However, it is successfully generating all necessary files(side
chain model, standard model and large model) but the name of 'Fe' atom in
Gaussian input is 'F' (which is for fluorine ). I followed your previous
post
http://archive.ambermd.org/201505/0351.html
where similar error was reported. As per your suggestion, changing atom
name and residue name as FE2, gives new error : key error: FE2-FE2 and in
this case necessary files for large model is not generated. Therefore, I
followed the previous step where atom name is FE and residue name is FE2
and I manually renamed F of Gaussian file as Fe and ran the optimization.
Please suggest me whether these files are okay to proceed for the next
stage of parameterization. I would be very thankful for your help.
Best regards
Kshatresh
On Mon, Sep 14, 2015 at 7:15 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Kshatresh,
>
> > Hi Pengfei,
> >
> > Sorry for multiple posting. I recompiled the MCPB program after
> installing
> > scipy and this fixes the program error. Many thanks for your help.
>
> No problem.
>
> > However,
> > it is showing error while running the my input as follows but gives all
> > necessarily files eg gaussian inputs for side chain and large model,
> > fingerprint files etc.
> > .......
> > ......
> > Creating the normal residue 387-S0H
> > Totally there are 106 atoms in the large model.
> > Totally there are 457 electrons in the large model.
> > Traceback (most recent call last):
> > File "/usr/local/amber14/bin/MCPB.py", line 419, in <module>
> > watermodel, 2, sqmopt)
> > File
> >
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> > line 1167, in gene_model_files
> > ionids, chargedict, totchg, outf, watermodel, sqmopt)
> > File
> >
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> > line 984, in build_large_model
> > chg = str(int(chargedict[i]))
> > KeyError: ‘FE'
> >
>
> Is the Fe ion in the FE.mol2 file has the same residue and atom names as
> it in the PDB file (e.g. all have “FE" as residue name and as atom name)?
>
> >
> > I followed the same input as in MCPB tutorial, changed the atom id for FE
> > according to pdb, produced WAT.mol2 files. However I am not sure how to
> add
> > WAT.mol2 file in input and there is no information about this in manual
> as
> > well. In addition I found that program MCPB assigns FE as Z1 in
> fingerprint
> > file generated by run.
>
> You can add WAT.mol2 file name after the naa_mol2files variable in the
> MCPB.py input file, it is fine for naa_mol2files variable following by
> several mol2 file names.
>
> MCPB.py will assign FE as Z1 automatically during the parameterization
> step if you pick the default mode for step 1, which will make the Fe ion
> has a unique atom type from other atoms. It is fine.
>
> >
> > Please help me regarding these issues. Thanks in advance.
> >
>
> Best,
> Pengfei
>
> > On Sun, Sep 13, 2015 at 5:11 AM, Kshatresh Dutta Dubey <
> kshatresh.gmail.com <mailto:kshatresh.gmail.com>>
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks for help. I found that python-scipy was not installed. I
> installed
> >> scipy but still I am facing some problem and now the error is :
> >> Traceback (most recent call last):
> >> File "/usr/local/amber14/bin/MCPB.py", line 46, in <module>
> >> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> >> ImportError: No module named mcpb.gene_model_files
> >>
> >> Please help me the to fix this issue.
> >>
> >> On Sun, Sep 13, 2015 at 2:30 AM, Pengfei Li <ambermailpengfei.gmail.com
> >
> >> wrote:
> >>
> >>> Hi Kshatresh,
> >>>
> >>> It seems the error implies that you did not install scipy in the
> machine.
> >>> Can you do a quick check by using the following command *python -c
> "import
> >>> scipy"*, if there is error raised, which means you did not install
> scipy
> >>> indeed.
> >>>
> >>> Best,
> >>> Pengfei
> >>>
> >>> 2015-09-12 10:45 GMT-04:00 Kshatresh Dutta Dubey <kshatresh.gmail.com
> >:
> >>>
> >>>> HI Pengfei,
> >>>>
> >>>> I am facing a new problem during MCPB.py run after installing
> AmberTool
> >>> 15.
> >>>> It seems to me something is wrong with python interpreter, but other
> >>>> programs like MMPBSA.py is running fine with same installations. I
> have
> >>>> correctly defined the python environment as it is mentioned in
> >>> amber.sh. I
> >>>> am getting following error during MCPB.py :
> >>>>
> >>>> Traceback (most recent call last):
> >>>> File "/usr/local/amber14/bin/MCPB.py", line 46, in <module>
> >>>> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> >>>> File
> >>>>
> >>>
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>>> line 13, in <module>
> >>>> from pymsmtlib.lib import get_lib_dict
> >>>> File
> >>> "/usr/local/amber14/lib/python2.7/site-packages/pymsmtlib/lib.py",
> >>>> line 8, in <module>
> >>>> from scipy.optimize import curve_fit
> >>>> ImportError: No module named scipy.optimize
> >>>>
> >>>> Please help me to figure out the problem.
> >>>>
> >>>> Thanking you
> >>>> Kshatresh
> >>>>
> >>>>
> >>>> On Fri, Sep 11, 2015 at 7:19 PM, Pengfei Li <
> ambermailpengfei.gmail.com
> >>>>
> >>>> wrote:
> >>>>
> >>>>> Hi Kshatresh,
> >>>>>
> >>>>> It also supports Zn. The following words in the tutorial may be
> >>>> confusing:
> >>>>>
> >>>>> Z-matrix methodThe bond and angle force constants are determined from
> >>> the
> >>>>> Cartesian Hessian matrixSeminario MethodThe bond and angle force
> >>>> constants
> >>>>> are determined from the sub matrices of the Cartesian Hessian
> >>>>> matrixEmpirical
> >>>>> Method (Only in MCPB.py)The bond and angle force constants are
> >>> determined
> >>>>> from an empirical method developed by Li et al. in Merz Research
> >>> Group,
> >>>>> current version only supports bonded model of Zinc ion
> >>>>>
> >>>>> Actually it means, MCPB supports two methods (Z-matrix and
> Seminario),
> >>>>> while MCPB.py supports three methods (Z-matrix, Seminario and an
> >>>> empirical
> >>>>> one). The empirical method in MCPB.py only supports Zn ion now but
> for
> >>>> the
> >>>>> other two methods in MCPB.py they support a lot of ions.
> >>>>>
> >>>>> Best,
> >>>>> Pengfei
> >>>>>
> >>>>> 2015-09-11 12:15 GMT-04:00 Kshatresh Dutta Dubey <
> kshatresh.gmail.com
> >>>> :
> >>>>>
> >>>>>> Hi Pengfei
> >>>>>>
> >>>>>> Thanks for your reply. Does the python version also support for Fe?
> >>>> Some
> >>>>>> time ago I read that present version supports only for Zn.
> >>>>>>
> >>>>>> On Fri, Sep 11, 2015 at 6:56 PM, Pengfei Li <
> >>>> ambermailpengfei.gmail.com>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Dear Kshatresh,
> >>>>>>>
> >>>>>>> There is a program called MCPB.py, a python substitute of MCPB, in
> >>>>>>> AmberTools15 (AmberTools15 is free and you can download it here:
> >>>>>>> http://ambermd.org/AmberTools15-get.html). It takes much less
> >>> time
> >>>> to
> >>>>>>> parameterize a metal site by using MCPB.py than MCPB. There is
> >>> also a
> >>>>> web
> >>>>>>> tutorial about MCPB.py:
> >>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm. If
> >>> you
> >>>>> have
> >>>>>>> more questions, please feel free to email me.
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Pengfei
> >>>>>>>
> >>>>>>>
> >>>>>>> 2015-09-10 16:25 GMT-04:00 Kshatresh Dutta Dubey <
> >>>> kshatresh.gmail.com
> >>>>>> :
> >>>>>>>
> >>>>>>>> Dear Users,
> >>>>>>>>
> >>>>>>>> I am using MCPB for building parameter of iron containing
> >>> protein.
> >>>> I
> >>>>> am
> >>>>>>>> following exactly the same steps as described in MCPB tutorial,
> >>>>>> however I
> >>>>>>>> am getting problem in copying StdResidue in during
> >>> _sidechain.bcl,
> >>>>>>>> particularly to the line describing metal (FE). I am
> >>> attaching my
> >>>>>>>> _sidechain.bcl as well as pdb file.
> >>>>>>>> Please help me to fix this problem
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> With best regards
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> ************************************************************************************************
> >>>>>>>> Kshatresh Dutta Dubey
> >>>>>>>> Post Doctoral Researcher,
> >>>>>>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>>>>>> Hebrew University of Jerusalem Israel
> >>>>>>>> Jerusalem, Israel
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Pengfei Li
> >>>>>>> Ph.D. Candidate
> >>>>>>> Merz Research Group
> >>>>>>> Department of Chemistry
> >>>>>>> Michigan State University
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> With best regards
> >>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> ************************************************************************************************
> >>>>>> Kshatresh Dutta Dubey
> >>>>>> Post Doctoral Researcher,
> >>>>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>>>> Hebrew University of Jerusalem Israel
> >>>>>> Jerusalem, Israel
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Pengfei Li
> >>>>> Ph.D. Candidate
> >>>>> Merz Research Group
> >>>>> Department of Chemistry
> >>>>> Michigan State University
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> With best regards
> >>>>
> >>>>
> >>>
> ************************************************************************************************
> >>>> Kshatresh Dutta Dubey
> >>>> Post Doctoral Researcher,
> >>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>> Hebrew University of Jerusalem Israel
> >>>> Jerusalem, Israel
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Pengfei Li
> >>> Ph.D. Candidate
> >>> Merz Research Group
> >>> Department of Chemistry
> >>> Michigan State University
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> With best regards
> >>
> >>
> ************************************************************************************************
> >> Kshatresh Dutta Dubey
> >> Post Doctoral Researcher,
> >> Lise Meitner Center for Computational Quantum Chemistry
> >> Hebrew University of Jerusalem Israel
> >> Jerusalem, Israel
> >>
> >>
> >>
> >
> >
> > --
> > With best regards
> >
> ************************************************************************************************
> > Kshatresh Dutta Dubey
> > Post Doctoral Researcher,
> > Lise Meitner Center for Computational Quantum Chemistry
> > Hebrew University of Jerusalem Israel
> > Jerusalem, Israel
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
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Received on Mon Sep 14 2015 - 11:00:03 PDT
