Dear Amber members:
Thank you very much for your time!
This is Mingyuan Xu, and now I am a PhD. student in East China Normal University. In my research,I want to build the force field parameters with MCPB.py tools to research the interaction between the Cu(1+) ions with azurin protein (a kind of Blue copper protein). In my system, there is an Oxygen atom on the backbone of the residue GLY45 that coordinated with Cu(1+) ion. The mcpb.py tool in amber14 could not deal with this case. Fortunately, I found your MCPB.py 2.0 on the GitHub website. And I have prepared all the files that are mentioned in step 1 of MCPB.py and I have finished the optimization and frequency calculation of the metal binding site successfully. But I meet some problems when I want to get the frcmod file in step2 with the Seminario method.
The MCPB.py program warned as shown in follows:
==================Using the Seminario method to solve the problem.
=======================Generate the bond parameters===============
For bondtype: Y1-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.84]
The average bond length is: 2.84 Angstrom.
The force constant(s) is(are): [0.0]
The average force constant is: 0.0 Kcal*mol^-1*A^-2.
For bondtype: Y2-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.0344]
The average bond length is: 2.0344 Angstrom.
The force constant(s) is(are): [0.0]
The average force constant is: 0.0 Kcal*mol^-1*A^-2.
For bondtype: Y3-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.2339]
The average bond length is: 2.2339 Angstrom.
The force constant(s) is(are): [0.0]
The average force constant is: 0.0 Kcal*mol^-1*A^-2.
For bondtype: Y4-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.1223]
The average bond length is: 2.1223 Angstrom.
The force constant(s) is(are): [0.0]
The average force constant is: 0.0 Kcal*mol^-1*A^-2.
For bondtype: Y5-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [3.1776]
The average bond length is: 3.1776 Angstrom.
The force constant(s) is(are): [0.0]
The average force constant is: 0.0 Kcal*mol^-1*A^-2.
=======================Generate the angle parameters==============
Traceback (most recent call last):
File "/home/myxu/soft/amber14/bin/MCPB.py", line 587, in <module>
fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
File "/home/myxu/soft/amber14/bin/mcpb/gene_final_frcmod_file.py", line 719, in gene_by_QM_fitting_sem
angval, fcfinal = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
File "/home/myxu/soft/amber14/bin/mcpb/gene_final_frcmod_file.py", line 421, in get_ang_fc_with_sem
fcfinal1 = get_ang_fc(afcmatrix12, afcmatrix32, vecPA,vecPC, dis12, dis32)
File "/home/myxu/soft/amber14/bin/mcpb/gene_final_frcmod_file.py", line 381, in get_ang_fc
contri12 = 1.0 / (contri12 * dis12 * dis12)
File "/home/myxu/soft/amber14/bin/parmed.py", line 35, in _print_warnings
if file is None: file = sys.stderr
AttributeError: 'NoneType' object has no attribute 'stderr'
I could get the frcmod file, but all the force constant of the coordinate bond is 0. The result is the same with the Z-matrix method. I don’t know whether there are mistakes in my calculation. all the calculation files are in the attachment.
So could you give me some advice?
It is really my great honor to receive your letter.
Thank you !
Give you my best wishes
Mingyuan Xu
2017.03.29
从网易163邮箱发来的云附件
MCPB_calculation.tar.gz (66.83M, 2017年4月13日 20:02 到期)
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Received on Wed Mar 29 2017 - 19:00:02 PDT
