[gmx-users] parameters for CH1 -- S -- CH2 ?
Mark.Abraham at anu.edu.au
Fri Aug 19 18:06:56 CEST 2011
On 20/08/2011 1:57 AM, Yun Shi wrote:
> 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?
Parameterizing new species is not easy. See
http://www.gromacs.org/Documentation/How-tos/Parameterization. Be sure
to check the literature for existing approaches - and particularly how
the thioether parameters that do exist were derived.
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