[gmx-users] top file for Gold

[kamil at ibmb.uni.wroc.pl]

You have to modify the residue topology file and also file with atom
definitions and add your atom type ...

There were some problems and questions about adding Mn earlier so check
the mailing archive, you should find the answer there...

Good luck !!!

On Sat, 20 Mar 2004, Keta Jones wrote:

> Dear gromacs users,
>
> I was struggling with my problem for making gold
> layers.
> I have created a pdb file of hydrogenated atoms.i.e
>
>      Au-Au-Au-Au-Au-Au-h
>
> Now I want to create top and rtp files for my system.
> So I type  the following command.
>
> x2top -f su.pdb -o au.top -r au.rtp
>
> Using  Gromacs Forcefield. Then the error message is
> as follows.
>
> Looking whether force field file ffgmx.rtp exists
> Opening library file
> /usr/local/gromacs/share/top/ffgmx.rtp
> Generating bonds from distances...
> Opening library file
> /usr/local/gromacs/share/top/ffgmx.atp
> There are 53 type to mass translations
> atom 7
> Opening library file
> /usr/local/gromacs/share/top/ffgmx.n2t
> There are 20 name to type translations
> Fatal error: No forcefield type for atom Au (1) with 0
> bonds
>
>
> So would please someone help how to proceed ?
>
> I also tried with pdb2gmx. but there error message is
> Fatal error: Residue 'Au' not found in residue
> topology database.
> I realize that I have do something for modifying
> /top/ffgmx.n2t file or something else.But I can not
> confirm waht to do . Please help.
>
> Thanks in advance,
> regards
> Keta
>
> =====
> Keta
> **************************************************************************************
>
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