Thanks Dr. Anselm for the suggestion.
I will write to the authors of these papers.
However, I think this question is well suited to this mailing list as well.
I think the collective knowledge of this list can be very useful for this issue and having an explanation here will help other amber users as well.
I am aware of the other charge derivation methods, and I am trying a couple of them, but this issue of charge neutralization after replacing the charges will come up in all approaches unless I decide to use the derived charges for the whole residue.
I have decent NMR data that I will use to validate the derived parameters.
Best,
Amin.
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Thursday, July 27, 2023 10:37 AM
To: amber.ambermd.org
Subject: SPAM: Re: [AMBER] How to neutralize charge after replacing the charges calculated by antechamber
This Message originated outside your organization.
Amin,
without going into detail, I'd suggest to contact authors of the many
studies in the literature you mentioned in order to learn, how they
achieved their goal. In that way, you had a procedure for charge
adaption you could refer to when describing your methods.
(Note that for atomic charge generation there exist several schemes and
procedures.)
However, you have to decide yourself whether this procedure works also
in your case; this might require running test/validation simulations for
your new parameters.
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 26.07.2023 um 18:54 schrieb Amin Sagar via AMBER:
> Dear Amber Community,
> I am trying to run MD simulations with a peptide which has a covalently modified cysteine. I followed the following steps.
>
> 1. I generated a mol2 of the modified residue, capped it with ACE and NME and calculated the charges using antechamber.
> 2. Since, I want to use ff15ipq for the simulations, I replaced the backbone charges and names using amino15ipq_10.0.lib.
> 3. Then, I generated an off file and modified it to have information about bonding to neighbouring residues.
> 4. I generated the missing parameters using parchchk2.
> I can now build systems using this residue, but it has a net charge of 0.23 as I replaced the charges in step2.
> This procedure seems to be followed in many studies in the literature.
> How is the charge neutralized in these cases? Should I just distribute the charge equally to all the other atoms, or is there a better way of doing this?
> Thanks.
>
> Amin Sagar
> Senior Computational Chemist
>
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