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

[Fernando Mattio]

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.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051017/fd797186/attachment.html>