Re: CHARMM36 parameters for nucelobases

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Sat Nov 10 2018 - 07:14:49 CST

You can generate the parameters by two methods, 1. You can write a patch to
create the required nucleobase from the available parameters in CHARMM.
2. You can use CHARMM-GUI for creating the parameters, but do look out for
the penalties associated, in most cases you might need to perform some
validation for the values that CHARMM-GUI gives you.

Best,
Hemanth H

On Sat 10 Nov, 2018, 6:37 PM Shivangi Nangia <
shivangi_nangia_at_remove_yahoo.com wrote:

> Hello,
>
> Where can I find CHARMM36 parameters for individual nucleobases.
> There is a RESI for AMP (Adenine Mono phosphate) in top_all36_cgenff.rtf
> and URAC for Urcail (not with the sugar attached).
> There are various other RESI where cytosine is attached to other moities
> (example:
> RESI NUSC 0.00 ! C9H13N3O4 nucleoside with cytosine)
>
> I need parameters for cytidine monophosphate, uradine monophosphate,
> thymidne monophosphate.
>
>
> Many thanks in advance for the help.
>
> Thanks,
> Shivi
>

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