Hi Yifei,
Thank you for the long waiting. I finally built a primitive tutorial for “using MCPB.py for systems with a modified residue” using 4CEU as an example (should work for 6rkg). Please follow the steps below:
1. Obtain the 4CEU PDB file.
2. pdb4amber -i 4ceu.pdb -o 4CEU_fixed_H.pdb --reduce (this step replaces H++ but might be problematic in future simulation)
3. Obtain KCX.cif from here<
https://www.rcsb.org/ligand/KCX>.
4. Follow the GFP tutorial to generate KCX.frcmod. The mc file is attached at the end for convenience.
5. Obtain KCX.mol2 using antechamber -fi ccif -i KCX.cif -bk KCX -fo mol2 -o KCX.mol2 -c bcc -at amber command.
6. Obtain NI.mol2, HOH.mol2 and OH.mol2 as the MCPB.py tutorial suggests. Some slight modification is needed since the system has two Nickels, and OH is not given. For your convenience, I attached all these files at the end.
7. Using parmchk2 -i <residue>.mol2 -o <residue>.frcmod -f mol2 to obtain the frcmod files for HOH and OH, respectively.
8. Name 4CEU files properly, especially the NI index. Make sure these three lines are included:
ion_mol2files NI.mol2
naa_mol2files OH.mol2 KCX.mol2 HOH.mol2
frcmod_files frcmod.OH frcmod.KCX frcmod.HOH
1. MCPB.py -i 4CEU.in -s 1. It should not generate any error. (I do not have a Gaussian license anymore, so I am learning GAMESS from scratch. It is giving some convergence error, but I believe that has something to do with my GAMESS command, not the system).
Hope it helps. Will keep you posted on the upcoming steps once I am able to handle GAMESS.
Best regards,
Zhen.
NI.mol2,
.<TRIPOS>MOLECULE
NI
1 0 1 0 0
SMALL
User Assigned Charge
.<TRIPOS>ATOM
1 NI 31.1550 72.7500 72.9000 NI 600 NI 2.000000
2 NI 27.5450 73.3810 72.7350 NI 601 NI 2.000000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 NI 1 TEMP 0 **** **** 0 ROOT
HOH.mol2
.<TRIPOS>MOLECULE
HOH
3 2 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 O -20.8680 9.1540 30.3470 OW 1 HOH -0.785000
2 H1 -19.9110 9.1540 30.3470 HW 1 HOH 0.392000
3 H2 -21.1080 10.0810 30.3470 HW 1 HOH 0.392000
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
.<TRIPOS>SUBSTRUCTURE
1 HOH 1 TEMP 0 **** **** 0 ROOT
OH.mol2
.<TRIPOS>MOLECULE
OH
2 1 1 0 0
SMALL
resp
.<TRIPOS>ATOM
1 O 0.0000 0.0000 0.1070 OW 1 OH -1.205795
2 H1 0.0000 0.0000 -0.8550 HW 1 OH 0.205795
.<TRIPOS>BOND
1 1 2 1
.<TRIPOS>SUBSTRUCTURE
1 OH 1 TEMP 0 **** **** 0 ROOT
kcx.mc
HEAD_NAME N
TAIL_NAME C
MAIN_CHAIN CA
OMIT_NAME H2
OMIT_NAME H
OMIT_NAME OXT
OMIT_NAME HXT
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0
From: Li, Zhen via AMBER <amber.ambermd.org>
Date: Wednesday, September 25, 2024 at 11:06 PM
To: 郑逸非 <20222002110062.stu.usc.edu.cn>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain)
Hi Yifei,
Thank you for being interested in MCPB.py. I have encountered a similar question before: “What if the metal center has a non-standard residue coordinating with it?”
The short answer is “customize this KCX residue and then feed the frcmod plus mol2 parameters to both MCPB.py’s and tleap’s input files”.
I agree that it is hard to do so, and the best tutorial that I can find is here<
https://urldefense.com/v3/__https://carlosramosg.com/amber-custom-residue-parameterization__;!!HXCxUKc!y5mmu5LiTU4flWyBWARRzXh_ngaNo6QF4IxPDe03_9tB7owxQGgvH-q-W-fIqp7JyVxvYbv3utnVD1L_mUqjgAg$ > for generating FRCMOD and here<
https://urldefense.com/v3/__https://pablito-playground.readthedocs.io/en/latest/tutorials/qmmm_amber_cpmd/mol2_file.html__;!!HXCxUKc!y5mmu5LiTU4flWyBWARRzXh_ngaNo6QF4IxPDe03_9tB7owxQGgvH-q-W-fIqp7JyVxvYbv3utnVD1L_L2Lv--E$ > for generating MOL2.
The FRCMOD generation already considered that the residue is linked to the main chain, while the MOL2 tutorial does not. This should be fine since linking to the main chain will not affect the MOL2 charge a lot, and the model will be sent to QM calculations anyway.
If all the attempts still fail. Please feel free to go with the QM/MM option. QUICK now supports many basis sets and functionals for transition metals.
I will be working on a tutorial about “MCPB.py with modified residue” soon.
Wish all the best.
Zhen.
>
> On Sep 23, 2024, at 10:31 PM, 郑逸非 via AMBER <amber.ambermd.org> wrote:
>
> Hello!
>
> I'm new to AMBER. I would like to know if it is possible to use MCPB.py for proteins containing nickel metal ions in the active site with non-standard residues in the backbone.
>
> Both examples “Building Bonded Model for A Ligand Binding Metalloprotein with MCPB.py” and “Building Bonded Model for A HEME Group with MCPB.py” are tutorials that deal with ligand molecules, metal ions, and water molecules independent of proteins. It doesn't seem to be possible to use the methods of the first two examples to work with structured molecule files. My question is what should I do when I encounter a structure that contains non-standard residues in the main chain with a metal site(PDB code:4CEU)? There is a LYSINE NZ-CARBOXYLIC ACID(KCX) in subunit α. Should I just replace it with lysine or is there another way? Any tutorials or simple steps to share? Thank you!
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Received on Sat Oct 26 2024 - 12:30:02 PDT
