[gmx-users] trouble with a triple bond
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 3 15:33:30 CEST 2009
Maybe this previous post will be of some use:
Alexander Bujotzek wrote:
> Dear all,
> I am experiencing some trouble with a small molecule containing a C-C
> triple bond, using a topology built by PRODRG beta. I intend to use
> ffG43a2, with a contraint on all bond lengths.
> Energy minization does not converge, as forces on the atoms involved in
> the bond seem to oscillate (not very high forces, though).
> Position restrained MD fails with LINCS errors,
> and unrestrained MD leads to a blow-up of the system.
> I guess the fault lies in the representation of the triple bond in the
> topology file, as a derivate of the molecule (with a single bond in the
> same place) works just fine.
> Excerpt from the itp building block provided by PRODRG beta. The triple
> bond is supposed to be between carbons 18 and 19:
> [ bonds ]
> 17 18 2 0.147 3422818.4 0.147 3422818.4 ; CAQ CAR 18
> 19 2 0.122 2309822.8 0.122 2309822.8 ; CAR CAS 20 19
> 2 0.147 3422818.4 0.147 3422818.4 ; CAT CAS
> [ angles ]
> 16 17 18 2 109.5 520.0 109.5 520.0 ; OAP CAQ
> 17 18 19 2 180.0 41840001.2 180.0 41840001.2 ; CAQ CAR
> 18 19 20 2 180.0 41840001.2 180.0 41840001.2 ; CAR CAS
> 19 20 21 2 109.5 520.0 109.5 520.0 ; CAS CAT
> There is no dihedral with 18 and 19 in the middle, but I assume that is
> correct as triple bonds are not supposed to be "rotatable"?
> What strikes me is the high force constant on the two 180 degree angles...
> may that be a source of error?
> Any help is appreciated! Maybe someone even has a working template of a
> correct triple bond topology at hand?
> Best regards and thank you for reading
> PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C
> triple bond... or maybe it's just the heat in my office.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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