[gmx-users] missing residues
spoel at xray.bmc.uu.se
Wed Mar 17 22:16:01 CET 2004
On Wed, 2004-03-17 at 18:33, Yu Sun (Denis) wrote:
> Dear gmx-users,
> I am dealing with a large protein (~ 75kD). There are some missing
> residues and atoms. For example, there are 9 residues missing in sequence (
> 21 to 29 ). I used InsightII to add all the missing residues and atoms.
> Then I am trying to use Gromacs to do energy minimization. But I got fmax =
> inf and energy is very high( positive 10^5).
> I took out residues from 20 to 30 to obtain a pdb file with 11
> residues and fixed residue 20 and 30 to do energy minimization (in vacuum),
> still got very high positive energy. When not fixing 20 and 30, negative
> energy can be obtained ( negative 10^3).
> Can anyone suggest me how to deal with such problems, i.e. add
> missing disordered residues in a pdb file and get reasonable structure?
You could put position restraints on the "good" coordinates and then run
in vacuum for a bit, maybe at zero K. Of course your starting coords
should not be complete nonsense. If this works then solvate the protein,
and simulate at 300 K, keeping the position restraints on the good bit
until the energy converges (maybe 50-200 ps). Then release the whole
> Yu Sun
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David van der Spoel, PhD, Assist. 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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