AMBER Archive (2005)

Subject: AMBER: how the phosphated threonine to be recognized in leap

From: haixiao jin (jinhx952_at_gmail.com)
Date: Thu Jun 23 2005 - 04:03:26 CDT

Dear Amber users,
Phosphate on residues is common phenomenon protein kinase. However,
FATAL is appeared in leap when I make the com.prmtop and com.inpcrd
files.
FATAL: ATOM .R<TPO197>. A <N1> does not have a type.
Additionally, the forcefield I used is leaprc.ff99.
the phosphated threonine is more than 5 Å from the inhibitor, to
mutate the TPO197 to THR197 is a way to solve the problem, but the
protein kinase requires a phosphate on Thr197 for optimal activity.
this phosphate anchors the activation loop in the proper comformation
and contributes to catalytic efficiency by enhancing the prosphoryl
transfer rate and increasing the affinity for ATP.
Then, how to solve the problem? How to make the the phosphated
threonine(TPO) to be recognized in leap? Thank you for your care!

Haixiao jin
A student from zhejiang university
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