[gmx-users] bonds

Erik Marklund erikm at xray.bmc.uu.se
Tue Sep 19 09:16:48 CEST 2006

Hi Elias,

A more detailed description of the actual error would make it a whole
lot easier for us to help out. Perhaps a copy of the actual error
message too.


On Mon, 2006-09-18 at 18:02 -0300, Elias santos wrote:
> Hi!
>  I have a question . I am working with a protein that they will count
> two
> centers FES co-ordinated for cisteins, these cisteins were not on to
> iron
> atoms, thus I modified the archive itp only with respect the bonds,
> no 
> angles or diedrals, to bind to these two residuos. After the
> minimização, I
> made one md with restricted position, when I make the total dynamic
> with I
> tie occurs error in the algorithm shake and it stops in the first
> steps 
> informing that I did not obtain to set molecules of water. I am using
> the
> field of force of gromacs (option 4) and the water is spc216.
>  ESS
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Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se

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