[AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines)

From: Christopher Corbo via AMBER <amber.ambermd.org>
Date: Mon, 5 Jun 2023 16:36:17 -0400

Hello Amber Users,

I have noticed a potential issue in amber16 & 20 for systems which contain
NAD and NAP (3 letter pdb codes) cofactors.

The issue arises because when I pass the mol2 into antechamber for bcc
charges, it overrides the bond orders for the Nicotinamide ring. Initially
the ring is passed in as fully aromatic, but the message is given:

Number of bonds (3) does not match connectivity (2) for N.ar N6

The bond from N.ar to C2N becomes “1” bond order and to C6N becomes “2”
bond order, while the remaining 4 bonds are still “ar”

Bcc charges are successfully calculated with overridden bond orders.

However when I take the processed mol2 (with overridden bond orders) and
pass it back into antechamber with -fo prepi to create a prep file, there
is a FATAL ERROR thrown for C2N because of an open valence (3). C2N has “1”
bond to N6, “1” bond to a H and “ar” bond to C3N.

When I manually adjust the bond orders back to all “ar” in the mol2 the
prep file is then handled and created successfully.

I have not tried this with amber22 yet.

Is there any auxiliary files which have been validated that I should be
using for NAD and NAP instead? Or is there a way to address this issue
within the software?

While I can manually fix this problem, I have been working on developing a
fully automated protocol for our lab to successfully rebuild our testset of
1000+ protein ligand systems.

Kind Regards,

Christopher Corbo
Christopher Corbo
Ph.D. Student
Department of Biochemistry and Structural Biology
Member of the Rizzo Lab
Stony Brook University
AMBER mailing list
Received on Mon Jun 05 2023 - 14:00:02 PDT
Custom Search