[gmx-users] trouble with a triple bond

[Justin A. Lemkul]

Maybe this previous post will be of some use:

http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html

-Justin

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
> CAR
>   17  18  19   2    180.0  41840001.2    180.0  41840001.2 ;   CAQ  CAR
> CAS
>   18  19  20   2    180.0  41840001.2    180.0  41840001.2 ;   CAR  CAS
> CAT
>   19  20  21   2    109.5       520.0    109.5       520.0 ;   CAS  CAT
> OAU
> ...
> 
> 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
> 
> Alex
> 
> 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.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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