[gmx-users] adding atom in .atp file

[Erik Lindahl]

Hi Magnus,

On Dec 11, 2005, at 4:07 PM, Magnus Andersson wrote:

> Hi all,
>
> After adding iodine to the ffG43a1.atp file I get the following 'error
> message' when running pdb2gmx:
>
> Looking whether force field file ffG43a1.rtp exists
> Opening library file ffG43a1.rtp
> Opening library file /usr/share/gromacs-3.2.1/top/aminoacids.dat
> Reading transiodoretinal.pdb...
> Read 4753 atoms
> Opening library file /usr/share/gromacs-3.2.1/top/xlateat.dat
> 23 out of 23 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 1 blocks of water and 3116 residues with  
> 4753 atoms
>
>   chain  #res #atoms
>   1 ' '  3090   4675
>   2 '-'    26     78  (only water)
>
> All occupancies are one
> Opening library file /usr/share/gromacs-3.2.1/top/ffG43a1.atp
> Atomtype 50  (which is my newly added iodine...)
>
> And it just stops... so I guess it's not really an error message.  
> What can
> be wrong here?

First, is shouldn't just hang, so please file a bugzilla.gromacs.org  
bug about that, preferably with example files to reproduce it.

For pdb2gmx you'll also need to add the ion as a molecule in the  
residue topology database (rtp file).

Cheers,

Erik
-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214