[AMBER] how to treat capped non-standard AA residue

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Tue, 11 Feb 2020 19:07:04 +0900

Dear All,
I have prepared Amber parameters for the extended CYS-Heme-Fe system using
G09-DFT calculations, esp files and resp fitting with antechamber (amber
atom types). Then I did manual atom-typing, atom reordering and
translation of the coordinates in mol2 file to match Heme coordiantes in
3v8d.pdb. As a result tleap is reading frcmod, mol2 files correctly and
generating parameter/inpcrd files.
But the CYS-HEME-Fe mol2 files contains N-CH3 and CO-H terminal caps, which
were added to run G09 calculations (to avoid scf convergence due to open

Now I think the prmtop/inpcrd file generated by above procedure have capped
CYS-Heme-Fe which I can't connect to the main-protein chain.
Thus my questions are the following.

1) How should I modify the mol2 file for CYS-Heme-Fe so that the N/C-cap
don't get added when leap generates the inpcrd/prmtops. Is it meaningful to
remove the N-*CH3* and CO-*H *atoms from this mol2 file?

2) Some parameters in frcmod where missing like radius for Fe, S which I
added manually from here
<http://abulafia.mt.ic.ac.uk/shannon/radius.php?Element=S>. But I don't
immediately understand how to derive the other bonded, non-bonded
parameters which antechamber/pramchk2 didn't find.

3) Which modification should be made in the PDB so that tleap doesn't add
the N/C-terminal caps and allows to connect the CYS with residues 420 and

All the files mentioned above are attached for your reference.
Looking forward for your valuable suggestions.
Thank you and best regards.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Tue Feb 11 2020 - 06:00:02 PST
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