[AMBER] Issues in Modified nucleotide parametrization using Antechamber and Parmchk2

From: Priyasha Majee via AMBER <amber.ambermd.org>
Date: Thu, 16 Nov 2023 18:54:08 +0530

Dear All,

we were trying to parameterize a modified nucleotide. We optimised the
structure in Gaussian as central residue without including the H in 03'
position. But it was showing double bond character between the O3' and
C3'. We were having incorporation issue so we reoptimized with H in O3'.
And during the incorporation in tleap, we removed HO3' using remove
command in tleap. however we had two major issues, This O3' is still
showing OH atom type and we get a warning while saving parameter file
which says unperturbed charge of 0.0812 is not integral.This happens
even after adding K+ charges.

1. is it okay to keep it same?

2. is it fine to manually change the OH atom type to OS in the mol2 and
prepi file and generate frcmod in parmchk2 followed by removal of HO3'
in tleap?

3. also we were not getting head and tail info in the mol2 file in
antechamber, so we were manually adding it. is this fine?

If not, could you suggest some way to work this out in Gaussian and

Since i am beginner, it would be helpful if you could point out any
error in the procedure or suggest any tutorial in the same line.
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Received on Thu Nov 16 2023 - 05:30:02 PST
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