[gmx-users] Restraining molecular symmetry
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
> 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?
> 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
> 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
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
More information about the gromacs.org_gmx-users