[gmx-users] Protein blowing apart

[David]

On Wed, 2005-09-14 at 14:01 -0700, Gia Maisuradze wrote:
> Do you mean I should make the whole protein as one block in the rtp, or add 
> pairs to the end units I've made in the rtp file?
Just make a new ALA definition, or if this (below) is everything you can
also use the prodrg server.
> 

> >>
> >> Ok well yes there are strong interaction pairs.  The structure is:
> >> (CH3)2-CO-/NH-CHCH3-CO-ALA-CO-NH-CCH3-CO/-NH-CH3
> >> The slashes indicate the custom groups that I added.  When I assemble
> >> this protein from a pdb file, it does not add bonds to the two ending
> >> groups.  Instead I go in to the *.top file and add bonds and angles.
> >> It also probably does not add pairs between these groups and the ALA's

-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++