David van der Spoel spoel at xray.bmc.uu.se
Sat May 18 10:43:21 CEST 2002

On Fri, 17 May 2002, Marc A Ceruso wrote:

>I need to build a palmitoylated cystein. The lipid group and the cysteine
>are covalently linked via a thioester linkage. I am facing two different
>    1- how to chose the charges on and near the thioester linkage:
>    Has anyone described such a chemical group?
I don't know this one.

>    2- If I use the lipid parameters (atom types and LJ) to describe the
>palmitoyl moiety then I need to generate the LJ14 "pairs" parameters (since
>they do not exist in the forcefieldand grompp assigns a value of zero for
>the incriminated LJ14 interactions ). Does anyone know how the values of the
>LJ14 parameters are generated?
They are identical to normal LJ, unless specified. Otherwise, pairs,
angles and dihedrals are generated. You may have to check what happens to
the linkage. Should that be planar? In that case you need an improper.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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