[AMBER] tleap gamma-carboxyglutamic acid linkage error

From: Rajbinder Kaur Virk <rajbinderkaurvirk.gmail.com>
Date: Mon, 22 Oct 2018 08:36:30 +0530

We were trying to use mcpb program of amber, in order to generate
force field parameters of a metaloprotein complex. After reaching the
final step, leap program was initiated. There is an unusual amino acid
in the protein, gamma-carboxyglutamic acid, to which leap program is
adding the missing terminal OXT group and breaking its peptide linkage
to other amino acids while building the missing hydrogen molecules.
I am quite new to this field, please pardon me for any mistake, I
wanted to inquire a) if we could build the parameter and force field
file for gamma-carboxyglutamic as given for the charmm force field
b) or if we can source charmm force field in leap
c) or if we can follow the scheme of using antechamber and parmcheck2
to generate the necessary files.
Further, we intend to use the sander program of amber.
Eagerly looking forward for suggestions
Thank you
With regards
Rajbinder Kaur Virk

*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
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Received on Sun Oct 21 2018 - 20:30:03 PDT
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