[AMBER] TI for DG when only cofactor charge changes

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Sun, 3 Oct 2021 11:51:35 +0530

Dear All,
I want to estimate DG for a charge transfer between two cofactors.
The reaction is RO --> OR (R is reduced and O is an oxidized state).
Is it possible to use TI simulations to do this?
Here the two topologies required for TI would differ only due to
differences in the charges (no atoms are morphed or mutated).
Section 25.1.8 asks to create a combined PDB from two states (redox states
in my case). Then to use leap to create prmtop/inpcrd.
My question is, how to differentiate the RO from the OR states while giving
parameter files (mol2 and frcmod) files?
I have these files in different directories but both have the same atom
type and residue names only charges are different.
Thus if I load files for R state first followed by O state, then parameters
for R state will be replaced by O state for both units while creating
prmtop/inpcrd for combined pdb.
Can you please suggest how to deal with this? I tried by giving unique
names to units in the PDB for O state and rename the same in the mol2 file
for O state?
It works for non-metal residues but gives errors for metal ions.

Looking forward to valuable suggestions from the list.

/home/user/Installations/amber20/bin/teLeap: Warning!
The unperturbed charge of the unit (1.210997) is not integral.

/home/user/Installations/amber20/bin/teLeap: Warning!
The unperturbed charge of the unit (1.210997) is not zero.
FATAL: Atom .R<FE2 1256>.A<FE 2> does not have a type.

/home/user/Installations/amber20/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 16; Notes = 0.

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

NCBI bibliography:


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Received on Sat Oct 02 2021 - 23:30:02 PDT
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