Dear Francois,
Thanks for letting me know about the PyRED. I tried it and worked well
except some of the bond information (attached to the metal atom) were
missing. I added them manually and obtained corresponding parameters from
Gaussian calculations.
Thanks again.
Regards,
Surya Prakash Tiwari
On Sat, Apr 9, 2016 at 4:28 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Surya Prakash Tiwari,
>
> You could use PyRED at R.E.D. Server Dev. to generate the required
> force field:
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> See Tutorials:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf
>
> regards, Francois
>
>
> > I am getting an error in step 2s. Please see the output below. I used
> > Gaussian 09. Any help will be greatly appreciated. If you need any other
> > input, please let me know.
>
>
> > st.hpcee:~/3_cat1oh_new$ MCPB.py -i 1cat.in -s 2
> >
> >
> >
> > ******************************************************************
> > * Welcome to use MCPB.py program *
> > * Author: Pengfei Li *
> > * Merz Research Group *
> > * Michigan State University *
> > * All Rights Reserved *
> > ******************************************************************
> >
> >
> >
> > The input file you are using is : 1cat.in
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > The following is the input variable you have:
> > The variable original_pdb is : full.pdb
> > The variable ion_ids is : [68]
> > The variable ion_mol2files is : ['ZN.mol2']
> > The variable group_name is : MOL
> > The variable cut_off is : 3.8
> > The variable ionchg_fixation is : 1
> > 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 : []
> > The variable naa_mol2files is : ['MOL.mol2', 'LIG.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: [1, 2, 64, 68]
> > 1-MOL.1-N : n2 --> X1
> > 1-MOL.2-O : o --> X2
> > 2-LIG.64-O : o --> X3
> > 3-ZN.68-ZN : ZN --> Z1
> > ==================Using the Seminario method to solve the problem.
> > Traceback (most recent call last):
> > File "/nfs/home/5/stiwari/softwares/amber14/bin/MCPB.py", line 434, in
> > <module>
> > g0x)
> > File
> >
> "/nfs/home/5/stiwari/softwares/amber14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py",
> > line 309, in gene_by_QM_fitting_sem
> > 'Force Field')
> > File
> >
> "/nfs/home/5/stiwari/softwares/amber14/lib/python2.7/site-packages/pymsmtmol/gauio.py",
> > line 47, in get_crds_from_fchk
> > crds.append(float(j))
> > ValueError: could not convert string to float: Force
> > st.hpcee:~/3_cat1oh_new$
> > st.hpcee:~/3_cat1oh_new$
> > st.hpcee:~/3_cat1oh_new$
> > st.hpcee:~/3_cat1oh_new$ ls
> > 1AMP_OH.in MOL_large_mk.com MOL_sidechain_fc.log
> > old resp2.in
> > 1cat.in MOL_large_mk.esp MOL_sidechain_opt.com
> > resp1_calc.esp resp2.out
> > acpype MOL_large_mk.log MOL_sidechain_opt.fchk
> > resp1.chg resp2.pch
> > full.pdb MOL_large.pdb MOL_sidechain_opt.log
> > resp1.in ZN.mol2
> > gaussian MOL_mcpbpy.pdb MOL_sidechain.pdb
> > resp1.out
> > LIG.mol2 MOL.mol2 MOL_standard.fingerprint
> > resp1.pch
> > MOL.frcmod MOL_pre.frcmod MOL_standard.pdb
> > resp2_calc.esp
> > MOL_large.fingerprint MOL_sidechain_fc.com naa
> > resp2.chg
> > st.hpcee:~/3_cat1oh_new$ MCPB.py -i 1cat.in -s 2
> >
> >
> >
> > ******************************************************************
> > * Welcome to use MCPB.py program *
> > * Author: Pengfei Li *
> > * Merz Research Group *
> > * Michigan State University *
> > * All Rights Reserved *
> > ******************************************************************
> >
> >
> >
> > The input file you are using is : 1cat.in
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > The following is the input variable you have:
> > The variable original_pdb is : full.pdb
> > The variable ion_ids is : [68]
> > The variable ion_mol2files is : ['ZN.mol2']
> > The variable group_name is : MOL
> > The variable cut_off is : 3.8
> > The variable ionchg_fixation is : 1
> > 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 : []
> > The variable naa_mol2files is : ['MOL.mol2', 'LIG.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: [1, 2, 64, 68]
> > 1-MOL.1-N : n2 --> X1
> > 1-MOL.2-O : o --> X2
> > 2-LIG.64-O : o --> X3
> > 3-ZN.68-ZN : ZN --> Z1
> > ==================Using the Seminario method to solve the problem.
> > Traceback (most recent call last):
> > File "/nfs/home/5/stiwari/softwares/amber14/bin/MCPB.py", line 434, in
> > <module>
> > g0x)
> > File
> >
> "/nfs/home/5/stiwari/softwares/amber14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py",
> > line 309, in gene_by_QM_fitting_sem
> > 'Force Field')
> >
> > File
> >
> "/nfs/home/5/stiwari/softwares/amber14/lib/python2.7/site-packages/pymsmtmol/gauio.py",
> > line 47, in get_crds_from_fchk
> > crds.append(float(j))
> > ValueError: could not convert string to float: Force
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu May 05 2016 - 11:00:03 PDT
