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

Fernando Mattio mattiofer at gmail.com
Mon Oct 17 11:03:22 CEST 2005

Hello Amol,
I think you can generate the .gro file from your .pdb file with:
editconf -f input.pdb -o output.gro
As I am a new user I don´t know yet what you can do with the topology file,
I also have the same problem because I would like to generate ice
topologies... But at least the .gro file I think it´s possible for you to
create. I holp it helps you,
Best regards,
Fernando Mattio

2005/10/17, Amol D. Atre <ssb4 at udct.org>:
> 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.
> Regards,
> Amol D. Atre.
> Lab No.A002,
> Chemical Engineering Department,
> Mumbai University Institute of Chemical Technology,
> Matunga(E), Mumbai-400019.
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