Dear Jon Uranga
Original MCPB.py can not
deal with the C-terminal or N-terminal cut modeling now.
But, Mr. Pengfei Li has pre-released a new version (v1.0 Beta2) of pyMSMT. It supports modeling for system which has N-terminal/C-terminal or backbone N or C atoms coordinated to metal ions. You may need to perform the modeling again from the beginning. You can check this webpage for how to get it: https://github.com/pengfeili1/pymsmt/wiki.
Best regards
Takeshi Baba
--------------------------------------------------------------------------------------------------------
Takeshi Baba
Division of Chemical Engineering,
Department of Materials Engineering Science,
Graduate School of Engineering Science,
Osaka University, Toyonaka, Osaka 560-8531, JAPAN
Tel: +81-6-6850-6266, Fax: +81-6-6850-6268
e-mail: tbaba.cheng.es.osaka-u.ac.jp
--------------------------------------------------------------------------------------------------------
On 2015/07/21, at 22:21, Jon Uranga <jonur9.gmail.com> wrote:
> 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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>
>
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Received on Tue Jul 21 2015 - 08:00:02 PDT
