Dear Amber users,
I follow the tutorial to set up my own system with the heme molecule.
(
Http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm)
All the first steps are well done. However, I have a problem when i
perform the RESP load fitting (MCPB.py -i 3LN0.in -s 3)
It appears that the message comes from a formatting problem of
"resp2.chg". There are also summation values in resp1.pch, resp1.chg (In
attachment)
Any help in this regard is highly appreciated.
Many thanks
Abdennour
Here is the output error message
******************************************************************
* Welcome to use the MCPB.py program *
* Version 3.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
* AND *
* Hammes-Schiffer Research Group *
* University of Illinois at Urbana-Champaign *
******************************************************************
The input file you are using is : 3LN0.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [8938]
The variable ion_info is : []
The variable ion_mol2files is : ['FE.mol2']
The variable original_pdb is : 3LN0_H_renum.pdb
The variable add_bonded_pairs is : []
The variable add_redcrd is : 0
The variable additional_resids is : []
The variable anglefc_avg is : 0
The variable bondfc_avg is : 0
The variable chgfix_resids is : []
The variable cut_off is : 2.8
The variable force_field is : ff14SB
The variable frcmod_files is : ['HEM.frcmod', '52B.frcmod']
The variable gaff is : 1
The variable group_name is : 3LN0
The variable ion_paraset is : CM (Only for nonbonded model)
The variable large_opt is : 1
The variable lgmodel_chg is : -99
The variable lgmodel_spin is : -99
-99 means program will assign a charge automatically.
The variable naa_mol2files is : ['HEM.mol2', '52B.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
The variable smmodel_spin 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
The variable xstru is : 0
******************************************************************
* *
*======================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/braka/anaconda2/envs/py34/bin/MCPB.py", line 684, in <module>
premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
File
"/home/braka/anaconda2/envs/py34/lib/python3.4/site-packages/pymsmt/mcpb/resp_fitting.py",
line 468, in resp_fitting
chgs = read_resp_file('resp2.chg')
File
"/home/braka/anaconda2/envs/py34/lib/python3.4/site-packages/pymsmt/mcpb/resp_fitting.py",
line 24, in read_resp_file
chgs.append(float(i))
ValueError: could not convert string to float:
'-55.964654165.030579-55.964654-55.964654'
========================================================================================
--
Abdennour BRAKA
/PharmD, PhD Student
Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA)
UMR CNRS-Université d'Orléans 7311
Université d'Orléans
Rue de Chartres
F-45067 Orléans
phone: +33 238 494 577/
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Received on Fri Jul 07 2017 - 08:00:02 PDT
