[gmx-users] Input for n-butanol molecule

[Justin A. Lemkul]

Juliana Angeiras wrote:
> Hi,
>  
> I'm having problem to prepare the archive molecule.itp for n-butanol below,
>  
> [ moleculetype ]
> ; name  nrexcl
> BuOH    3
>  [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr        charge          mass
>      1      opls_079  1   BuOH     HO     1       0.435
>      2      opls_078  1   BuOH     OH     1      -0.700
>      3      opls_081  1   BuOH     CA     1       0.265
>      4      opls_071  1   BuOH     CB     1       0.000
>      5      opls_071  1   BuOH     CC     1       0.000
>      6      opls_068  1   BuOH     CD     1       0.000
>  [ bonds ]
> ;  ai    aj funct           c0           c1
>    1    2   1   0.09450   462750.4
>    2    3   1   0.13640   376560.0
>    3    4   1   0.15040   265265.6
>    4    5   1   0.15040   265265.6
>    5    6   1   0.15040   265265.6
>  [ angles ]
> ;  ai    aj    ak funct           c0        c1
>   4     3     2   1    109.500    418.400
>   3     2     1   1    108.500    460.240
>   5     4     3   1    112.700    488.273
>   6     5     4   1    112.700    488.273
> [ dihedrals ]
>   1  2  3  4  1    0.41840   1.25520   0.00000  -1.67360   0.00000   0.00000
>   2  3  4  5  1    2.87441   0.58158   2.09200  -5.54799   0.00000   0.00000
>   3  4  5  6  1    2.92880  -1.46440   0.20920  -1.67360   0.00000   0.00000
>  
> But I have obtained the following message with the grompp:
>  
> Fatal error:
> A non-integer value (2.092000) was supplied for 'multiplicity' in Proper 
> Dih.

The dihedral function type 1 specifies a periodic proper dihedral, which should 
then list phi, k, and multiplicity.  It appears the terms listed are for a 
Ryckaert-Bellemans dihedral (Cn coefficients), so the type should be changed to 
3 instead of 1.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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