[gmx-users] trouble with a triple bond

[Alexander Bujotzek]

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
and C20:

[ 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.

Regards,

Alex


>
> 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.
>
> --
> ========================================
>
> 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
>
> ========================================
>


-- 
Alexander Bujotzek
Zuse Institute Berlin
Computational Drug Design Group
Tel. : +49 30 84185-234
eMail: bujotzek at zib.de