[gmx-users] Ammonia-Water

Amol D. Atre ssb4 at udct.org
Sat Oct 1 12:23:37 CEST 2005

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

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?

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.

Amol D. Atre.
Lab No.A002,
Chemical Engineering Department,
Mumbai University Institute of Chemical Technology,
Matunga(E), Mumbai-400019.

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