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

From: He, Amy via AMBER <amber.ambermd.org>
Date: Fri, 17 Nov 2023 04:05:54 +0000

Hi Priyasha,

I recommend taking a quick look at the following tutorial on parameterization of a modified amino acid residue:
https://ambermd.org/tutorials/basic/tutorial5/
This tutorial can get you some general idea how to parameterize a linking embedded fragment in a biomacromolecule.


Regarding your questions:

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'.

H is fine, or you can cap the O3’ by a phosphate group to maintain the geometry and charge density nearby.


And during the incorporation in tleap, we removed HO3' using remove command in tleap / we get a warning while saving parameter file which says unperturbed charge of 0.0812 is not integral / also we were not getting head and tail info in the mol2 file in antechamber, so we were manually adding it. is this fine?

You can (1) exclude the capping groups, (2) set the head and tail, and (3) correct the total charge using `prepgen`. See Section 3 in the above tutorial.


is it fine to manually change the OH atom type to OS in the mol2 and prepi file

In theory you could manually change atom types to do some hacky things 😊 But you shouldn’t need to, if you have passed the head and tail information through the mainchain file (.mc) for `prepgen`.


Hope this is mildly helpful..

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Lab
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
From: Priyasha Majee via AMBER <amber.ambermd.org>
Date: Thursday, November 16, 2023 at 8:25 AM
To: Amber <amber.ambermd.org>
Subject: [AMBER] Issues in Modified nucleotide parametrization using Antechamber and Parmchk2
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
antechamber?
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 - 20:30:02 PST