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/
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Received on Sat Apr 09 2016 - 01:30:06 PDT
