[gmx-users] parameters for CH1 -- S -- CH2 ?

Yun Shi yunshi09 at gmail.com
Fri Aug 19 17:57:57 CEST 2011

Hi all,

I have a small molecule with a part like:

CH1 --- CH1 --- S --- CH2 --- CH1

I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and
dihedral parameters according what are already present in the
gromos53a6.ff/ffbonded.itp file. Since this file does not contain
information regarding this CH1 --- S --- CH2 pattern, PRODRG just assigned
bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- CH2 pattern,
and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if it was CH1 -- CH2
-- S -- CH2.

So I guess I have to do this manually. But as no corresponding parameters
defined in ffbonded.itp file, should I derive these parameters via chemical
intuition and try validate them in some way?

Or is there an easier alternative way to do this?

Thanks for any suggestion!

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