> Mark > > Hi Mark and other users, > > Thanks for your reply and apologies for my English. > > If the chain identifiers are discarded by gromacs why do I than get > from trjconv an output file looking like this when having more than one > chain in the .trr file like in this example (part of .pdb file) > > ATOM 2776 O1 PHE A 336 32.109 64.621 29.258 1.00 0.00 > ATOM 2777 O2 PHE A 336 30.372 64.241 30.505 1.00 0.00 > ATOM 2778 N THR B 337 60.139 23.423 46.095 1.00 0.00 > ATOM 2779 CA THR B 337 58.765 23.151 45.661 1.00 0.00 > > but not when I have only one chain in the .trr like in this example > (part of .pdb file). > > ATOM 2776 O1 PHE 336 41.051 55.857 23.785 1.00 0.00 > ATOM 2777 O2 PHE 336 42.809 56.115 22.532 1.00 0.00
That surprises me, maybe I've misunderstood something about how this all works. Certainly the .gro/.g96 formats do not have chain identifiers, so one possiblity was that the first .trr was generated from an grompp -c struct.pdb and the second from grompp -c struct.gro (or maybe mdrun -c similarly). > VMD can unfortunately not do what I need so is there no way to get the > chain identifier like in the first example? Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
