Thanks, That worked perfectly!
Regards,
Teri (Eleftherios) Lambros
On Fri, Jul 31, 2015 at 1:50 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> The problem has been solved, it is due to one ligand, which coordinate to
> the center metal ion, has the atoms of the same element with the same atom
> name. When one prepare a PDB file be used with MCPB.py, please make sure
> that the non-standard residues have each atom with different atom name.
>
> 2015-07-28 23:26 GMT-04:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
> > Hi Teri,
> >
> > Can you send me the related files? I can try to debug the code.
> >
> > Best,
> > Pengfei
> >
> > 2015-07-27 15:36 GMT-04:00 Eleftherios A P Lambros <tlambros.uci.edu>:
> >
> >> Hello,
> >>
> >> I am getting a mismatch error on the 3rd step of MCPB.py as follows,
> >>
> >> Input script
> >> MCPB.py -i TS3.in -s 3b
> >>
> >> Output..
> >> The input file you are using is : TS3.in
> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >> The following is the input variable you have:
> >> The variable original_pdb is : WTDBD_TS3_CU_protonated.pdb
> >> The variable ion_ids is : [3011]
> >> The variable ion_mol2files is : ['CU.mol2']
> >> The variable group_name is : TS3
> >> The variable cut_off is : 2.8
> >> The variable chgfix_resids is : []
> >> The variable scmodel_chg is : -99
> >> -99 means program will assign a charge automatically.
> >> The variable lgmodel_chg is : -99
> >> -99 means program will assign a charge automatically.
> >> The variable software_version is : g09
> >> The variable sqm_opt is : 0
> >> The variable large_opt is : 0
> >> The variable force_field is : ff14SB
> >> The variable gaff is : 1
> >> The variable frcmodfs is : ['TS#.frcmod']
> >> The variable scale_factor is : 1.0
> >> Attention: The force constants will be scaled by
> >> multiplying the square of scale_factor.
> >> The variable bondfc_avg is : 0
> >> The variable anglefc_avg is : 0
> >> The variable naa_mol2files is : ['TS#.mol2']
> >> The variable software_version is : g09
> >> The variable water_model is : TIP3P
> >> The variable ion_paraset is : CM (Only for nonbonded model)
> >> The variable ion_info is : []
> >> ******************************************************************
> >> * *
> >> *======================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...
> >> =========================Checking models==========================
> >> ***Check the large model...
> >> Good. The charges and atom numbers are match for the large model.
> >> Good. There are 57 atoms in the large model.
> >> ***Check the standard model...
> >> Traceback (most recent call last):
> >> File "/mnt/net_share/home/tlambros/amber15-with-patches/bin/MCPB.py",
> >> line 581, in <module>
> >> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
> >> File
> >>
> >>
> "/mnt/net_share/home/tlambros/amber15-with-patches/lib/python2.7/site-packages/mcpb/resp_fitting.py",
> >> line 517, in resp_fitting
> >> raise pymsmtError('Error: the charges and atom numbers are mismatch
> '
> >> pymsmtexp.pymsmtError: Error: the charges and atom numbers are mismatch
> >> for
> >> the standard model!
> >>
> >> Looking at the most recent call we have,
> >>
> >> if len(stlist) != len(stdict):
> >> raise pymsmtError('Error: the charges and atom numbers are
> mismatch
> >> '
> >> 'for the standard model!')
> >>
> >> Where stlist and stdict are generated as follows,,,
> >>
> >>
> >> metcenres1 = [] #original name of the metal center residue
> >> stlist = [] #get the atom name list from the standard model
> >> stf = open(stfpf, 'r')
> >> for line in stf:
> >> if line[0:4] != "LINK":
> >> line = line.strip('\n')
> >> line = line.split()
> >> stlist.append(line[0])
> >> line = line[0].split('-')
> >> lresname = line[0] + '-' + line[1]
> >> if lresname not in metcenres1:
> >> metcenres1.append(lresname)
> >> stf.close()
> >>
> >> llist = [] #get the atom name list from the large model
> >> lf = open(lgfpf, 'r')
> >> for line in lf:
> >> line = line.strip('\n')
> >> llist.append(line)
> >> lf.close()
> >>
> >> ldict = {} #get charge of the large model, one-to-one relationship
> >> for i in range(0, len(llist)):
> >> ldict[llist[i]] = chgs[i]
> >>
> >> stdict = {} #get the charge of the standard model
> >> for i in ldict.keys():
> >> if i in stlist:
> >> stdict[i] = ldict[i]
> >>
> >>
> >> >From my understanding, MCPB.py will generate an atom and charge list
> from
> >> the large model from the large model pdb and resp files respectively. To
> >> generate the charge list for the standard model, it takes atoms from the
> >> standard model, and if there exists the same atom in the large model, it
> >> assigns that atom its corresponding charge from the large model charge
> >> list. That is, the standard model is a proper subset of the large
> model. I
> >> have checked to my standard model pdb and fingerprint files and they are
> >> not missing or have any extra atoms. (The tutorial files worked just
> fine
> >> for this step) I compared the format of the corresponding pdb and
> >> fingerprint files from the tutorial and found no difference in format
> >> (i.e.
> >> the standard models had complete residues etc...)
> >>
> >> The previous steps worked so I assume my gaussian 09 calculations went
> >> without any problems. Any help on this is appreciated.
> >>
> >> *NOTE* I am using the developmental release of pymsmt
> >>
> >> Thanks,
> >> Teri (Eleftherios) Lambros
> >> --
> >> Mathematics, School of Physical Sciences
> >> Biochemistry and Molecular Biology, School of Biological Sciences
> >> University of California: Irvine
> >>
> >> President, Anteaters Mathematics Club
> >> Advocacy Committee, Biological Sciences Student Council
> >> _______________________________________________
> >> 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
> >
>
>
>
> --
> 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
>
--
Mathematics, School of Physical Sciences
Biochemistry and Molecular Biology, School of Biological Sciences
University of California: Irvine
President, Anteaters Mathematics Club
Advocacy Committee, Biological Sciences Student Council
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Received on Mon Aug 03 2015 - 14:00:02 PDT
