[gmx-users] xtal-water

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?
see above.

>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.

Groeten, David.
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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