[gmx-users] Restraining molecular symmetry

Alok Sharma aloks at mbu.iisc.ernet.in
Sat Jul 5 00:54:13 CEST 2008

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


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