Boron atom type is not present neither in GAFF neither in AMBER force field. Is there any ff implementation to parameter Boron? Do you have any suggestions to solve out the problem?
Hello Pasquale,
I think one of the ways for parametrizing it would be to optimize the ligand and compute the frequencies. Then, one could compute the bonded force constants as explained in detail in: Seminario, J. M. (1996), Calculation of intramolecular force fields from second‐derivative tensors. Int. J. Quantum Chem., 60: 1271-1277. Take a look at MCPB in amber, you may use that one.
For the non bonded interactions, I think, it is a bit more complex. You could still employ antechamber to do a resp charge fitting , but the lennard jones parameters might be more challenging. Maybe, you could run thermodynamic integration to fit them. The following article may be of your interest: Steinbrecher, J. T., Latzer, J. and Case, D. A. Chem. Theory Comput. 2012, 8, 11, 4405-4412.
Hope it is helpful!
Bests,
Jon
I have parametrized a BODIPY dye. Drop me a message, I may send them to you, if they are what you're looking for.
I tried to add partial charges to a ligand-containing boron for molecular docking, it is given error. Again, I tried to run antechamber but it not working. can someone please help.
Adeniyi Thompson Adewumi : Antechamber services several sub-programs to generate not only the RESP charges, but also to assign atom types, etc. With a boron in the molecule, the automatic procedure may fail. What kind of error it gives? Does antechamber generate any files?
A priori and without knowing the error I am guessing that it is because the boron atom is not being recognized. You may try running antechamber, disabling acdoctor (-dr no) and modifying the atom type and bond type prediction (-j 5). But then you need to be even more careful about the assigned atom types and the bond types.
Dear Dr. Michal H. Kolář,
Please I would appreciate it if it ould be helpful. You can email them to me on [email protected]. Thank you
Dear Jon Uranga,
The error is detailed below:
The error: Warning: For atom (ID: 10, Name: B02) the best APS is not zero
0, chain A: enoyl-[acyl-carrier-protein] reductase [nadh]
Chain-initial residues that are actual N terminii:
Chain-initial residues that are not actual N terminii:
Chain-final residues that are actual C terminii:
Chain-final residues that are not actual C terminii:
1 hydrogen bonds
Hydrogens added
Charge model: AMBER ff14SB
Assigning partial charges to residue 9JA (net charge +0) with am1-bcc method
Atom whose IDATM type has no equivalent Sybyl type: #-2147483648.-2147483648:1@B02 (type: B)
Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\student\appdata\local\temp\tmpv9_iby\ante.in.mol2 -fi mol2 -o c:\users\student\appdata\local\temp\tmpv9_iby\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(LIG) Welcome to antechamber 17.3: molecular input file processor.
(LIG) Info: Finished reading file (c:\users\student\appdata\local\temp\tmpv9_iby\ante.in.mol2).
(LIG) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(LIG) Warning: For atom (ID: 10, Name: Boron-Oxygen (B02) the best APS is not zero.
(LIG) Bonds involving this atom are frozen.
(LIG) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(LIG) Info: Total number of electrons: 236; net charge: 0
(LIG) Info: The number of electrons is odd ().
(LIG) Please check the total charge (-nc flag) and spin multiplicity (-m flag).
(LIG) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out
(LIG) /usr/bin/antechamber: Fatal Error!
(LIG) Cannot properly run ""C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out".
Failure running ANTECHAMBER for residue LIG
Check reply log for details
Dear Michal H. Kolář ,
What kind of error it gives?
For atom (ID: 10, Name: B02) the best APS is not zero . And Bonds involving this atom are frozen.
Does antechamber generate any files? NO , Failure running ANTECHAMBER for residue LIG
Dear Pasquale,
How did you solve the problem? I am dealing with a similar problem.
Adeniyi Thompson Adewumi
I recommend you using Multiwfn (http://sobereva.com/multiwfn) to calculate RESP charge, please check Section 4.7.7 of the manual for usage example. Multiwfn can very easily generate RESP charge for any kind of molecule containing any element, as long as you provide wavefunction file (e.g. .fch/.wfn/.wfx/.molden) generated by quantum chemistry code (e.g. Gaussian, ORCA, GAMESS).
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