A correction for this email:
The way to solve the problem is extracting the Fe ion out from the HEM
residue as an independent residue with residue name "FE" and atom name
"FE". In this way the software could recognize the Fe ion normally. You can
transfer the PDB file to mol2 file using antechamber and define the atom
type (recommend to use "FE") and charge (+2 or +3) of Fe ion inside the
mol2 file.
2015-05-20 10:21 GMT-04:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi David,
>
> Sorry for the late reply. Here the main thing is the program consider the
> Fe atom in HEM as a F atom. This bug dues to that I made all the element
> inside a residue except ion residues use the first letter as its element.
>
> The way to solve the problem is extract the Fe ion out from the HEM
> residue as an independent residue with residue name "FE" and atom name "FE"
> if it is Fe3+ or residue name "FE2" and atom name "FE2" if it is Fe2+. In
> this way the software could recognize the Fe ion normally.
>
> You may also try the existing parameters suggested by Dave. It would be a
> quick way to build the model and also a good way to do a quick check about
> whether the newly generated parameters by MCPB.py are correct.
>
> Hope that helps,
> Pengfei
>
> On May 19, 2015, at 1:46 PM, David Poole <thepoole.ucdavis.edu> wrote:
>
> > Hello all,
> >
> > I've been attempting to use the MCPB.py tool-chain to build amber
> > parameters for a iron porphyrin IX, heme, system, and have been having a
> > few difficulties that may be related.
> >
> > Like others in the past, I optimized a truncated system lacking the
> > propionate groups and bound to imidazole and carbon monoxide ligand. This
> > was optimized with using restricted DFT 631G** B3LYP, which worked just
> > fine.
> >
> >> From there I added the propionate groups and produced the MK charges
> from
> > an energy calculation at the same theory level.
> >
> > This was all good so I started with MCPB.py since Amber15 had just come
> out
> > and it appeared to be the best option for generating accurate parameters
> > for the iron center.
> >
> > I made the PDB file for the whole system from the optimized structure and
> > the iron / naa mol2 files from those produced with the MK charges using
> > UCSF Chimera maintaining the input atom types. I had some error with the
> > mol2 files due to formatting differences but I ran them through
> antechamber
> > to produce files that seemed to work correctly. I used the mol2 files and
> > antechamber to also generate the starting frcmod file.
> >
> > Then I ran MCPB.py with my input file (g09 was specified) and there was a
> > key error called for 'FE', I looked through and tried altering the
> > capitalization which resulted in a error called for 'HEM-Fe' which then
> > somehow decided afterwards to be simply 'Fe' in the next attempt.
> >
> > Gaussian input files were still produced so I thought to run it anyway.
> the
> > iron had been changed to a flourine so I corrected this and let it run
> > overnight on the cluster while I dozed. I had modified the optimization
> to
> > an energy calculation at the previous level of theory because the
> problems
> > the propionates would produce otherwise (pesky charged groups) and read
> the
> > esp fitting checkpoint file in as an initial guess to speed things along.
> > The freq input was also fixed to use the same level of theory as
> everything
> > else.
> >
> > This was successful.. but then when I ran step 2 using both z and s
> > options... it kicked back another key error when writing the pre.frcmod
> > file for 'F-2'.
> >
> > I am not sure how to proceed, but there is definitely a problem with some
> > formatting involving my iron core.
> >
> > Output from step 1:
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > The following is the input variable you have:
> > The variable original_pdb is : imz-carboxyheme-1.pdb
> > The variable ion_ids is : [9]
> > The variable ion_mol2files is : ['imz-carboxyheme-1_fe.mol2']
> > The variable group_name is : hem
> > The variable cut_off is : 2.8
> > The variable ionchg_fixation is : 0
> > The variable gau_version is : g09
> > The variable sqm_opt is : 0
> > The variable force_field is : ff14SB
> > The variable gaff is : 1
> > The variable frcmodfs is : ['imz-carboxyheme-1_ph.frcmod']
> > The variable naa_mol2files is : ['imz-carboxyheme-1_ph.mol2']
> > The variable water_model is : TIP3P
> > The variable ion_paraset is : CM (Only for nonbonded model)
> > The variable ion_info is : []
> > ******************************************************************
> > * *
> > *=======================Metal Site Information===================*
> > * *
> > ******************************************************************
> > ***Selected Metal ion Fe is atom 9 in residue 1-HEM
> > 1-HEM.N2 is in 2.8 Angstrom of 1-HEM.N2
> > 1-HEM.N3 is in 2.8 Angstrom of 1-HEM.N3
> > 1-HEM.N4 is in 2.8 Angstrom of 1-HEM.N4
> > 1-HEM.N5 is in 2.8 Angstrom of 1-HEM.N5
> > 1-HEM.N6 is in 2.8 Angstrom of 1-HEM.N6
> > ***The following residues are in the Metal Site:
> > Residue 1-HEM
> > ***The large model contains the following residues:
> > [1]
> > ******************************************************************
> > * *
> > *=======================Building models==========================*
> > * *
> > ******************************************************************
> > ***Creating the sidechain model...
> > It contains the residue 1-HEM
> > Totally there are 88 atoms in the sidechain model.
> > Totally there are 359 electrons in the sidechain model.
> > ***Creating the standard model...
> > It contains the residue 1-HEM
> > Totally there are 88 atoms in the standard model.
> > ***Creating the large model...
> > Creating the normal residue 1-HEM
> > Totally there are 88 atoms in the large model.
> > Totally there are 359 electrons in the large model.
> > Traceback (most recent call last):
> > File "/yggdrasil/amber14/bin/MCPB.py", line 419, in <module>
> > watermodel, 2, sqmopt)
> > File
> >
> "/yggdrasil/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> > line 1167, in gene_model_files
> > ionids, chargedict, totchg, outf, watermodel, sqmopt)
> > File
> >
> "/yggdrasil/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> > line 984, in build_large_model
> > chg = str(int(chargedict[i]))
> > KeyError: 'Fe'
> >
> >
> >
> >
> > Output from step 2:
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > The following is the input variable you have:
> > The variable original_pdb is : imz-carboxyheme-1.pdb
> > The variable ion_ids is : [9]
> > The variable ion_mol2files is : ['imz-carboxyheme-1_fe.mol2']
> > The variable group_name is : hem
> > The variable cut_off is : 2.8
> > The variable ionchg_fixation is : 0
> > The variable gau_version is : g09
> > The variable sqm_opt is : 0
> > The variable force_field is : ff14SB
> > The variable gaff is : 1
> > The variable frcmodfs is : ['imz-carboxyheme-1_ph.frcmod']
> > The variable naa_mol2files is : ['imz-carboxyheme-1_ph.mol2']
> > The variable water_model is : TIP3P
> > The variable ion_paraset is : CM (Only for nonbonded model)
> > The variable ion_info is : []
> > ******************************************************************
> > * *
> > *===================Generate the Initial frcmod file=============*
> > * *
> > ******************************************************************
> > Atoms which has changed the atom types: [5, 9, 14, 22, 30, 38]
> > 1-HEM.5-N2 : n2 --> X1
> > 1-HEM.9-Fe : Fe --> Z1
> > 1-HEM.14-N3 : n2 --> X2
> > 1-HEM.22-N4 : n2 --> X3
> > 1-HEM.30-N5 : n2 --> X4
> > 1-HEM.38-N6 : n2 --> X5
> > Traceback (most recent call last):
> > File "/yggdrasil/amber14/bin/MCPB.py", line 446, in <module>
> > gaff, frcmodfs, watermodel)
> > File
> >
> "/yggdrasil/amber14/lib/python2.7/site-packages/mcpb/gene_pre_frcmod_file.py",
> > line 369, in gene_pre_frcmod_file
> > rmin = IonLJParaDict[element + chg][0]
> > KeyError: 'F-2'
> >
> >
> > Thanks everybody!
> > -David Poole
> > M.Sc. San Francisco State University
> > _______________________________________________
> > 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
Received on Tue May 26 2015 - 10:00:03 PDT
