[gmx-users] trouble with a triple bond
bujotzek at zib.de
Mon Jul 6 17:08:49 CEST 2009
Thanks for the help, I think it worked out.
Just for the record:
For my chain-like molecule
...- C17 - C18 # C19 - C20 - ... (# = triple bond)
I defined C18 and C19 to be virtual sites defined by the positions of C17
[ virtual_sites2 ]
; Site from funct a
18 17 20 1 0.353365385
19 17 20 1 0.646634615
And constrained the distance between C17 and C20 to be the sum of the
three original bonds shown above:
[ constraints ]
; index1 index2 funct length(nm)
17 20 1 0.416
However, I had to set the mass of the "non-virtual" particles C18 and C19
to zero, as Gromacs demands virtual sites have no mass.
So technically speaking, my molecule has lost weight. I hope that doesn't
lead to artefacts, but as of now trajectories are looking good.
> 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
>> 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
Zuse Institute Berlin
Computational Drug Design Group
Tel. : +49 30 84185-234
eMail: bujotzek at zib.de
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