[gmx-users] aromatic hydrogens

Joanne Hanna J.F.Hanna at warwick.ac.uk
Thu Apr 27 16:29:34 CEST 2006


I have a question which has been puzzling me regarding the addition of hydrogens to atoms in aromatic rings. I am using force field ffG43a2 but do not have the GROMOS96 manual which is i assume the place to check how the force field was derived (please correct me if i am wrong) and I am confused as to why in a PHE residue all hydrogens (HC) are added to the carbons (C) in the aromatic group but in histidine, these carbon/hydrogen atoms are represented as atom typr CR1. This is mainly in connection to a topology that I have created of AMP, in which I have represented atoms 2C and 8C of the adenine ring as CR1 (on the guidance of Prodrg and the AMP topology in ffG43a2.rtp) and am now wondering whether these atoms should in fact be represented as explicitly as HC and C.
Could any one give me any feedback on any of this and why would be most appropriate to do in line with the ffG43a2 force field.

Many thanks

Joanne Hanna
Department of Chemistry
University of Warwick

(02476) 574623
J.F.Hanna at warwick.ac.uk

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