[gmx-users] Protein blowing apart

David spoel at xray.bmc.uu.se
Thu Sep 15 07:52:46 CEST 2005

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:
> >> 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 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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