[gmx-users] Topology for hetroatom (PRODRG)

David spoel at xray.bmc.uu.se
Wed Feb 23 07:40:43 CET 2005

On Wed, 2005-02-23 at 11:52 +0530, Alok wrote:
> hello David,
>                    Thank you for your reply.So we will include our 
> linker section molecule in the rtf and hdb files.But we are still not 
> sure of the parameters we are to take for the linker molecule.Should I 
> directly take the parameters mentioned in the ' itp file ' generated by 
> the PRODRG server ??????
>                           The linker section forms a covalent bond with 
> the peptide.The carbonyl group at both ends of the peptide 
> (XXX-NH-CH2-CH2-NH-XXX) forms a covalent bond with the amino group at 
> the ends of the linker section.
It depends on your force field. 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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