[gmx-users] Removal of Hydrogen atoms from the molecule??

Amol D. Atre ssb4 at udct.org
Mon Oct 17 10:47:08 CEST 2005

Hello all,

Tried to create topology (.top) and coordinate (.gro) files of 1 NH3
molecule using PRODRG program available online. But the program removes
all the Hydrogen atoms and returns an error that it does not support
mono/di atomic molecules.

Can anybody explain to me the significance of removal of Hydrogen atoms (I
mean why they are removed?). Does it mean that one cannot generate .top
and .gro files for a single molecule like NH3 or H2O? and one has to have
more than two molecules in order to generate .top and .gro files.

Waiting for suggestions/replies eagrly as I am badly stuck with this problem.

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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