[gmx-users] absent pairs

David spoel at xray.bmc.uu.se
Tue Jan 27 17:21:01 CET 2004

On Mon, 2004-01-26 at 19:32, Milton Taidi Sonoda wrote:
> Hi all
> I'm simutating a single 1,2-methanediol in a periodic box
> with OPLS forcefield.
> I've noted that the pairs of sites HO-HC were absent while all
> the other pairs were present in
> the pairs section of the topology file automatically generated
> with pdb2gmx. Is it rigth?

it seems highly unlikely that you could generate a topology for that
molecule with pdb2gmx. it is probably nonsense. 

> thank you in advance
> Milton Taidi Sonoda
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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