From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Sat Jun 26 2010 - 02:45:09 CDT
This _might_ work, but if it does, the results would be inaccurate at best. You need to get charmm27 parameters and charges for urea. Someone may already have them, or you may need to make them yourself.
This is not easy, so it would be best to google for the topology and parameters first.
Philip Peartree
University of Manchester
Sent from my iPhone
On 26 Jun 2010, at 02:05, "lixb07_at_lzu.cn" <lixb07_at_lzu.cn> wrote:
> Dear all:
>
> I am using NAMD to do molec ular dynamics simulation of a biological system which
> includes protein, lipid and urea. However, in CHARMM force field
> (top_all27_prot_lip.rtf and par_all27_prot_lip.prm), there is no related
> parameters for urea. So, is it correct to copy all parameters of urea from CGenFF
> force field and simply paste them in top_all27_prot_lip.rtf and
> par_all27_prot_lip.prm, according to their order? Should I need other
> modifications to make my system work normally? I would highly appreciate for your
> help! Thank you very much.
>
> Sincerely
>
> Xubin Li
> Lanzhou University
> China
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:16 CST