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

[Justin Lemkul]

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
>
>
>
>
>
>
>
> --
> 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.
>

-- 
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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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