David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 15 20:32:48 CET 2002
On Fri, 15 Mar 2002 nesanfor at criba.edu.ar wrote:
> I am trying to solvate a molecule wich was resolved vy x-ray diffraction
>with N cristallographic waters. To include those water in the solvation box I
>run the genbox with -cs -cp -ci an the option -nmol N -try 30
1st. leave the xtal water in. pdb2gmx will generate hydrogen positions for
them that you can optimize with energy minimization. Then add waters with
>a) As it seems that I have no guarantee that all the xtal-W will be set... (Is
>this right or wrong?)
correct with genbox.
>b) ... is there any other way to include the xtal-W in the solvation box?
>c) How can I manage to build a box with a cosolvent (say DMSO)?
use genbox with a dmso box. if you need mixed solvent, make a mixed
solvent first and then give that to genbox.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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