Dear all,
I am trying to parametrize the following monster, a copper bound cyclen ring derivative, with 47 heave atoms ligand (figures and mol files attached). This gentlemen is a little difficult, and I would like if possible to check and improve the procedure I am trying to use to produce frcmod and mol2 files output from antechamber and parmchck:
1) Create and optimize this guy using ChemAxon (mol file attached)
2) docked this guy into topoVI with autodock
3) run antechamber for the best docked conformation
4) run parmchk
5) used mol2 and frcmod files (both attached) to run MD with its target protein + DNA + CU
So I obtained the charges from antechamber and the frcmod, and was able to produce a prmtop etc, using the non-bonded model for CU, but I am still not very confident about this procedure:
1) Is this procedure correct? Can be improved? how?
2) Is the frcmod correct? For example in the attached figures I show the ligand with its atom names in mol2, and a certain dihedral angle that correspond to the following line on the frcmod file:
c3-c3-nh-ca 1.1 180.0 2.0 Using the default value
If I am not wrong, this angle can only between C2-N2-C10-C11 or C2-N2-C13-C12 since N2 is the only nh in this ligand, but then when I measure this dihedral it is 125 in my docking output, or 145 in the minimized structure (before docking), in any case is not 180.
3) What is going on here? Do I need to correct by hand this angle? Is there anything I need to pay attention to?
Thanks a lot in advance, any suggestion will be more than welcomed.
Best,
Fabian
Fabian Glaser PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/ <
http://bku.technion.ac.il/>
Tel +972 (0) 4 8293701
Best,
Fabian
Fabian Glaser PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
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Received on Mon Jun 24 2019 - 05:30:03 PDT
