AMBER Archive (2009)

Subject: [AMBER] validation of parameters and request suggestions

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Tue Mar 24 2009 - 06:52:19 CDT

Dear AMBER users,

    I am going to perform MD simulation of a protein-cofactor system, where the parameters of the cofactor is not included in the ff. So the antechamber module was used to obtain the parameters. Since there was a sulfonium group in the cofactor, the bonding, angle, dihedral, torsional and vdw parameters of this group were reset in the cofactor.frcmod file based on the work in BioChem, 2002, 41, 7636, in which the sulfonium group were parameterized in accordance with amber ff.

   Energy minimization and MD simulation (5ns) of the cofactor in complex with the protein showed that the conformational change of the cofactor wrt the initial structure was very small. My questions are,
1. As shown by the results of the conformational change, are the parameters obtained via the above procedure reasonably good for MD simulation?

OR

2. Since in above procedure I adopted the atomic charges (including the sulfonium group) produced by ANTECHAMBER, is it necessary to re-parameterize the atomic charges of this cofactor using RESP algorithm?

Thanks for the time.

-----
Jeffrey

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