Re: [AMBER] GLH with HE1

From: He, Amy via AMBER <>
Date: Wed, 1 Feb 2023 23:39:21 +0000

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.


From: He, Amy via AMBER <>
Date: Wednesday, February 1, 2023 at 6:24 PM
To: AMBER Mailing List <>
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 He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University<>
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Received on Wed Feb 01 2023 - 16:00:02 PST
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