Re: serine phosphorylation modeling

From: L. Michel Espinoza-Fonseca (
Date: Sat Nov 10 2007 - 19:15:40 CST

Dear Wei,

> I need to model two phosphorylated serine residues in a peptide before
> simulation. In the CHARMM stream file toppar_prot_na_all.str, I found two
> patches regarding this, SP1 and SP2, which contain net charges of -1 and -2
> respectively. Who can tell me which patch is better applied to my case and
> why?

It depends on the conditions you're going to simulate. For instance,
if you are planning to run a MD simulation of a peptide under
"physiological" conditions, the SP2 patch will be recommended. The SP1
patch is used for lower pH conditions (i.e., an "acidic" system). In
summary, the choice will basically depend on the pH of your system.

Good luck!

> Thank you
> Wei Liu

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