Dear Amber users,
I have been trying to set up some parameters for a Cu2+ containing system:
covalently bound to HID6, HID13 and ASP1. The ASP1 residue is bounded by
the side chain carboxylate and the carbonyl and the terminal nitrogen from
the backbone (one hydrogen from the N terminal has to be removed). In order
to proceed with such calculation I have downloaded the PDB of the protein
and added by hand the Cu2+. Then, I performed a QMMM geometry optimization
so that to obtain proper parameters for MM. Afterwards, I used MCPB.py in
order to obtain such parameters. However, I got some unexpected error:
******************************************************************
* 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 : 1IYT.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable original_pdb is : 1IYT_CU.pdb
The variable ion_ids is : [627]
The variable ion_mol2files is : ['CU.mol2']
The variable group_name is : 1IYT
The variable cut_off is : 5.0
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 : []
The variable water_model is : TIP3P
The variable ion_paraset is : CM (Only for nonbonded model)
The variable ion_info is : []
******************************************************************
* *
*=======================Metal Site Information===================*
* *
******************************************************************
***Selected Metal ion CU is atom 627 in residue 43-CU
1-ASP.N is in 5.0 Angstrom of 1-ASP.N
1-ASP.OD1 is in 5.0 Angstrom of 1-ASP.OD1
1-ASP.OD2 is in 5.0 Angstrom of 1-ASP.OD2
1-ASP.O is in 5.0 Angstrom of 1-ASP.O
2-ALA.N is in 5.0 Angstrom of 2-ALA.N
6-HID.ND1 is in 5.0 Angstrom of 6-HID.ND1
6-HID.NE2 is in 5.0 Angstrom of 6-HID.NE2
13-HID.ND1 is in 5.0 Angstrom of 13-HID.ND1
13-HID.NE2 is in 5.0 Angstrom of 13-HID.NE2
***The following residues are in the Metal Site:
Residue 1-ASP
Residue 2-ALA
Residue 6-HID
Residue 13-HID
Residue 43-CU
***The large model contains the following residues:
[0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 43]
******************************************************************
* *
*=======================Building models==========================*
* *
******************************************************************
***Creating the sidechain model...
It contains the residue 1-ASP
It contains the residue 2-ALA
It contains the residue 6-HID
It contains the residue 13-HID
It contains the residue 43-CU
Totally there are 51 atoms in the sidechain model.
Totally there are 191 electrons in the sidechain model.
***Creating the standard model...
It contains the residue 1-ASP
Traceback (most recent call last):
File "/usr/local/amber14/bin/MCPB.py", line 419, in <module>
watermodel, 2, sqmopt)
File
"/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 1164, in gene_model_files
libdict, autoattyp)
File
"/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
line 355, in build_standard_model
attype = libdict[resname + '-' + atname][0]
KeyError: 'ASP-H1'
It seems that it is not comfortable with the hydrogens from the terminal N.
I tried adding manually two glycines to the N terminal (now the terminal is
a GLY residue) and as far as the cutoff in the MCPB.py input file does not
take any terminal residue it works. Nevertheless, that is not the system I
am interested in. Could anyone provide any solution to this issue, I would
appreciate it.
Thank you!
Jon Uranga
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Received on Tue Jul 21 2015 - 06:30:02 PDT
