Dear Amber users,
I am trying to parameterize Zn coordinated to HID, HID, GLU and a water molecule and have been following the AMBER advanced tutorial 20 on MCPB.py.
The sidechain model geometry was optimized, force constants calculated for the large model and the sidechain model fchk file generated.
Next, the Merz-Kollman RESP charge calculation was done followed by the Gaussian 09 bug fix and espgen in AMBER.
The tutorial mentions that you should confirm that coordination bonds do not break. How do I check for this?
In the final modelling step using the gaussian output I get the following error:
[llubbe.login2 04072017_MCPBpycontd]$ MCPB.py -i 03072017_NDOM.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 : 03072017_NDOM.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable original_pdb is : 03072017_NDOM_H_All_renum.pdb
The variable ion_ids is : [9749]
The variable ion_mol2files is : ['ZN_renum.mol2']
The variable group_name is : NDOM
The variable cut_off is : 2.8
The variable ionchg_fixation is : 0
The variable gau_version is : g03
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 : ['WAT.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: [5694, 5750, 6151, 9749, 9750]
361-HID.5694-NE2 : NB --> X1
365-HID.5750-NE2 : NB --> X2
389-GLU.6151-OE1 : O2 --> X3
613-ZN.9749-ZN : ZN --> Z1
614-WAT.9750-O : OW --> X4
==================Using the Seminario method to solve the problem.
Traceback (most recent call last):
File "/apps/chpc/chem/amber/14/bin/MCPB.py", line 434, in <module>
g0x)
File "/apps/chpc/chem/amber/14/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py", line 306, in gene_by_QM_fitting_sem
'Int Atom Types')
File "/apps/chpc/chem/amber/14/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
Any advice on how to solve this would be greatly appreciated!
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Tue Jul 04 2017 - 04:30:03 PDT
