On 2/12/13 8:37 AM, durdagis wrote:
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).
OK, this was not clear from the picture you showed. The text in the
representation is not very legible, so it seemed like the bond length was
normal. If, after energy minimization, the bond length is incorrect, you should
stop and investigate its source:
1. Is the bond present in the topology? Bonds can only occur within a single
[moleculetype] so multiple chains must be merged appropriately with pdb2gmx options.
2. Are you using constraints during EM?
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?
Go back and solve the EM issue before blindly plowing ahead.
-Justin
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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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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