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
>
> -
>
> BicycleTx Ltd
> Blocks A & B
> Portway Building, Granta Park
> Cambridge CB21 6GS
>
> amin.sagar.bicycletx.com<mailto:amin.sagar.bicycletx.com>
> www.bicycletherapeutics.com<https://www.bicycletherapeutics.com/>
>
> [Bicycle]
>
> Twitter<https://twitter.com/bicycle_tx> | LinkedIn<https://www.linkedin.com/company/bicycle-therapeutics/>
>
> CONFIDENTIALITY NOTICE - This communication, including any attachments, is for the exclusive use of the intended recipient and may contain proprietary, confidential or privileged information. If you are not the intended recipient, any use, copying, disclosure, dissemination or distribution is strictly prohibited. If there is any reason to believe you are not the intended recipient, please notify the sender immediately by return email and delete this communication and destroy all copies. Thank you.
> BicycleTx Ltd. Company number 11036101. Registered in England.
>
> Disclaimer
>
> The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful.
>
> This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 27 2023 - 03:00:02 PDT
