explict water models

abonvin abonvin at igc.phys.chem.ethz.ch
Fri Aug 2 03:37:13 EST 1996

>I would like to set up a layer of explicitly defined waters around a protein
>model.  Could anyone tell me how to go about this using xplor.  Ideally I would
>like to have a 4-10 angstrom layer of water molecules and later set up a more
>relevant physiological buffer surrounding the protein.  Any advice will be
>greatly appreciated.
>Regards Paul.

Jiang's answer refers to X-ray refinement and solvent mask generation.
If you intend to run MD simulations with explicit water you need another
script (which should run with 3.1). You need therefore first an equilibrated
water box or sphere. Assuming that you have an equilibrated box of water
the script overlay_h2o_sphere.inp in 
http://igc.ethz.ch/abonvin/xplor_inp/H2O_DYNA should do the job. You can 
find in there other X-PLOR script for water simulations setups.

PS: You can find in the same directory a small box of equlibrated TIP3P water


| Dr. Alexandre Bonvin           | Phone: Int+41-1-632-5504              |
| Physical Chemistry, ETHZ       | Fax:   Int+41-1-632-1039              |
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| 8092 Zurich, Switzerland       | http://igc.chem.ethz.ch/abonvin       | 

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