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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
