[gmx-users] Ammonia-Water

[David]

On Sat, 2005-10-01 at 15:53 +0530, Amol D. Atre wrote:
> Hello all,
> 
> Created pdb file of single molecule of Ammonia using Ghemical in Linux. It
> looks like following,
> 
> ATOM      1  N   UNK     1      -0.000  -0.000   0.000  1.00  0.00
> ATOM      2  H   UNK     1      -0.909   0.582   0.000  1.00  0.00
> ATOM      3  H   UNK     1       0.959   0.496   0.000  1.00  0.00
> ATOM      4  H   UNK     1      -0.050  -1.079   0.000  1.00  0.00
> END
> 
> What should be put at the place of the Residue entry UNK (unknown) in
> order to create .gro and .top files of Ammonia? My ultimate aim is to
> solvate one Ammonia molecule in some number of molecules of Water using
> genbox program. Can anybody help me regarding how this can be done?
You have to do it manually (making the top file). See chapter 5.
Alternatively you can use the prodrg server.

> 
> My idea is as follows,
> Create Ammonia.gro
> Create Water.gro
> and then run
> 
> -cp Ammonia.gro -cs Water.gro -o Ammonia-Water.gro -p Ammonia-Water.top
> 
> Can anybody tell me whether this will work out or not?
> 
> Thanking in advance.
> 
> Regards,
> Amol D. Atre.
> Lab No.A002,
> Chemical Engineering Department,
> Mumbai University Institute of Chemical Technology,
> Matunga(E), Mumbai-400019.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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