From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Jun 16 2014 - 10:23:02 CDT
The answer to that question has not changed since last time you asked it.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2591.html
The recommendation is still to use standard CHARMM amide atom types and
charges. Among other places, the charges can be found in RESI NMA in
stream/toppar_all36_prot_model.str . When removing a nonpolar hydrogen to
free up a valence for the purpose of creating a bond to another nonpolar
group, we sum the charge of the hydrogen into the parent atom, as
documented at many places. Be careful when doing that, because in many
instances, atom types change when removing hydrogens.
On 06/14/2014 05:15 AM, Sadegh Faramarzi Ganjabad wrote:
> Hello
>
> I have connected side chain of ASP residue to side chain of LYS by a patch
> to get a cyclic peptide; an oxygen atom of ASP side chain and two hydrogen
> atom of LYS are deleted and the resulting patch is
>
> 1HB1 1HB2
> \ /
> --1CB
> \
> 1CG==OD1
> \
> 2NZ- 2HZ1
> |
> 2HE2 - 2CE- 2HE1
> |
>
> However, I'm wondering how should I assign atomic partial charges to this
> part of molecule. ASP was negatively charged before patch to LYS which was
> positively charged. Do you have any idea about how to update partial
> charges after patch?
>
> Thanks in advance
> Sadegh
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