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
|
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.
Mark
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