[gmx-users] Re: additional bond description (isopeptide bond) between two chains

[durdagis]

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







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