Dear all,
I can think of some walkaround:
(1) To simulate the syn- protomer with HE1:
Rename OE1, HE1 and OE2 so that the starting structure is just a different rotamer;
(2) To simulate the anti- protomers:
I will try the rename-atom trick. I think as long as the connectivity is intact (OE2 – HE2), other bonded parameters will be applied to the corresponding atom types.
The additional question I have is:
Is that ok for a dual-topology TI simulation, in which I’m trying to transform one protomer to another? Will I be able to get the “mixed” potential? Or will that become a single-topology TI simulation? I don’t think that could work since my HE2 is disappearing, and appearing at the same time… :’((
Can you please help? Any comments/suggestions would be greatly appreciated.
Bests,
Amy
From: He, Amy via AMBER <amber.ambermd.org>
Date: Wednesday, February 1, 2023 at 6:24 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] GLH with HE1
Dear Amber Community,
I am using Amber 20 and I intend to use leaprc.protein.ff14SB as the source of parameters for the standard residues in my protein.
I have a quick question about simulating a protonated glutamate residue (GLH) with a proton on OE1. By default (in lib file “amino12.lib”, residue GLH has a proton named HE2 on OE2 and the configuration is syn.
If I want to simulate GLH with HE1, or the anti- conformational isomers, do I have to make the nonstandard residues myself? Or is there any existing lib and/or frcmod files I can use in complementary to ff14SB?
Many Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
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Received on Wed Feb 01 2023 - 16:00:02 PST
