[gmx-users] pdb2gmx

[Kukol, Andreas]

You need to create your topology file manually and have a look at this:

http://wiki.gromacs.org/index.php/Exotic_Species

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of RAJAVARMAN.K
> Sent: 09 May 2008 15:34
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pdb2gmx
>
>  Respected sir,
>
>                    am  working with gold cluster .am planing to simulate
> gold cluster in the presence of vacuum.but i can,t able to convert the pdb
> file into gro,top format caz of the following statement"  Residue '2' not
> found in residue topology database ".
>
>                     i already gone through gromacs mailing list as well as
> gromacs manual 5 chapter.but i really don't know what to change in .rtp,.top
> files. so plz help me .am attaching my  error statement as well as input
> file.already have  experience  in working with protein,peptides,domain.but
> this is first time am using  metal cluster ( i.e 40 atoms of gold).can u
> please kindly help me by creating gold cluster topology,gro file.
>
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