Hi,
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.
Thanks.
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
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Received on Fri Apr 08 2016 - 11:30:03 PDT
