AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: David A. Case (
Date: Wed Feb 18 2004 - 13:34:24 CST

On Wed, Feb 18, 2004, L Jin wrote:

> The type of H54 is HO 'hydroxyl group' within parm99. And in my molecule it is
> attached to the oxygen which is part of the sulfate group, -SO3H. I have
> introduced the atom type for the S atom. And O41 is OS in parm99 too. The
> positions of H54 and O41 are like this R-O41-SO3H54. Both of the parms of H54
> and O41 are from Parm99. Do I need to modify the VDW parm? Thanks

This is a common problem with protonated versions of sulfate and phosphate
groups: the standard parameters bring a proton too close to one of the
neighboring oxygens. Adding a vdW radius will fix the crash, but doesn't
still give very good geometries. We have sometimes resorted to adding
an artificial "bond" between the S(P) and the hydrogen; this keeps the S-O-H
angle pretty much fixed, and can help. Basically, you are making your own
force field here, and you need to study its properties carefully.

...good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to