serine phosphorylation modeling

From: Wei Liu (wei.liu_at_biosci.ki.se)
Date: Sat Nov 10 2007 - 11:22:36 CST

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Dear all namd users,

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?

Thank you
Wei Liu

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