[gmx-users] Restraining molecular symmetry

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jul 5 09:34:11 CEST 2008


If you want to see the symmetry as in the crystal, try and simulate the crystal.
It may well be that in the absence of crystal packing forces a certain
degree of asymmetry is favourable.


On Sat, Jul 5, 2008 at 12:54 AM, Alok Sharma <aloks at mbu.iisc.ernet.in> wrote:
> Dear All,
> I have two queris
> First:
> I am simulating a tetramic protein, each monomer with 150 amino acids, in
> gromacs 3.3.1. The protein molecule has a proper 4 fold symmetry. But during
> simulation the symmetry is some what not retained. Two monomers which should be
> related by ~180 degree rotation, as seen in all the crytal structuers of the
> protein, gets oriented ~160 degrees. I am just wondering whether in gromcas
> there is an option to restrict/restrain the symmetry of the molecule (similar to
> non-crystallographic symmetry in crystallographic refinments). One way of doing
> this seems to restrain the back-bone which is not desired in the present case.
> Can any body suggest a way to restrain monomers, just to maintain the symmetry?
> Second:
> For a 20 ns simulation trajectory I want to calculate  water mediated hydrogen
> bonds between two monomers. I used -ins flag with g_hbond with following
> command...
>  g_hbond -f protein.xtc -s protein.tpr -n index.ndx -ac -dist -ang -hx -hbn -hbm
> -don -dan -life -nhbdist -ins -a 30 -r 0.36 -da.
> All the calculations are okay. Also an insert.dat file is created but it does
> not show any solvent insertion. I selected solvent group also for insertion
> correctly when prompted. But at least with some of the snap shots which I saw, I
> can find water mediated hydrogen bonds...Is there any other way to calculate
> solvent mediated hydrogen bonds..
> Thanks in advance for your suggestions
> Alok
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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