Justin, it's not the artifacts of visualization program. At the beginning distance for isopeptide bond is 1.38 Angs (and it's defined at the specbond.dat);
LYS NZ 1 GLY C 1 0.13 LYQ GLQ together with energy minimization this distance increases to around 3.0 Angs. (with normal termination). However, when I continue to run for md sim. I am getting several LINCS warnings (actually these relative constr. deviations are not at the isopeptide bond). Any suggestions how to handle this problem? Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.031846, max 1.324710 (between atoms 4480 and 4482) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Back Off! I just backed up step0b.pdb to ./#step0b.pdb.3# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.3# Wrote pdb files with previous and current coordinates Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.038596, max 1.704050 (between atoms 4504 and 4506) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4531 4546 57.3 0.2247 0.2305 0.1522 4531 4533 57.8 0.2243 0.2225 0.1526 -- View this message in context: http://gromacs.5086.n6.nabble.com/additional-bond-description-isopeptide-bond-between-two-chains-tp5005445p5005455.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
