[gmx-users] Topology for hetroatom (PRODRG)

[David]

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.
________________________________________________________________________
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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