RE: CHARMM36 parameters for nucelobases

From: Lennart Nilsson (Lennart.Nilsson_at_ki.se)
Date: Sat Nov 10 2018 - 10:24:29 CST

An single nucleotide (I.e. not just a nucleobase, but nucleobase+sugar+phosphate) is just a one-nucleotide “oligo”nucleotide, so it should work to specify a sequence with just one A (C/G/U) with 5’ phosphate and 3’-OH termini, alll of which are part of the standard CHARMM36 FF


Best wishes,
Lennart Nilsson


From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of HEMANTH H 18310019
Sent: den 10 november 2018 14:15
To: shivangi_nangia_at_yahoo.com
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: CHARMM36 parameters for nucelobases

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<mailto: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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