Dear Li Pengfei and Amber users,
I am interested in deriving parameters for an active site containing heme (Fe attached to 4 porphyrin N, 1 bonded with proximal His and 1 with ligand named UNK), so I followed the tutorial 20 provided by Pengfei Li & Kenneth M. Merz Jr. at Amber website. Everything went fine until I used “MCPB.py -i mcpb.in -s 3” to perform the RESP charge fitting and generate the mol2 files for the metal site residues. Some errors displayed:
$ MCPB.py -i mcpb.in -s 3
******************************************************************
* Welcome to use the MCPB.py program *
* Version 2.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
******************************************************************
The input file you are using is : mcpb.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [6459]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : complex_renum.pdb
The variable add_bonded_pairs is : []
The variable additional_resids is : []
The variable anglefc_avg is : 0
The variable bondfc_avg is : 0
The variable cut_off is : 2.8
The variable chgfix_resids is : []
The variable force_field is : ff14SB
The variable frcmodfs is : ['HEM.frcmod', 'UNK.frcmod']
The variable gaff is : 1
The variable group_name is : complex_mcpb
The variable ion_paraset is : CM (Only for nonbonded model)
The variable large_opt is : 1
The variable lgmodel_chg is : -99
-99 means program will assign a charge automatically.
The variable naa_mol2files is : ['HEM.mol2', 'UNK.mol2']
The variable scale_factor is : 1.0
ATTENTION: This is the scale factor of frequency. The
force constants will be scaled by multiplying the square
of scale_factor.
The variable smmodel_chg is : -99
-99 means program will assign a charge automatically.
The variable software_version is : g09
The variable sqm_opt is : 0
The variable water_model is : TIP3P
******************************************************************
* *
*======================RESP Charge fitting=======================*
* *
******************************************************************
***Generating the 1st stage resp charge fitting input file...
***Generating the 2nd stage resp charge fitting input file...
***Doing the RESP charge fiting...
Traceback (most recent call last):
File "/home/zou/amber16/bin/MCPB.py", line 600, in <module>
premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
File "/home/zou/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py", line 468, in resp_fitting
chgs = read_resp_file('resp2.chg')
File "/home/zou/amber16/lib/python2.7/site-packages/mcpb/resp_fitting.py", line 24, in read_resp_file
chgs.append(float(i))
ValueError: invalid literal for float(): 4.596714-13.654077
Any help in this regard is highly appreciated.
Many thanks
Allen Zou
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Received on Mon Sep 26 2016 - 18:00:02 PDT
