[gmx-users] [gmx-user]Error by pdb2gmx

[Mark Abraham]

----- Original Message -----
From: 佘安奇   <she_angel at yahoo.cn>
Date: Wednesday, May 19, 2010 16:17
Subject: [gmx-users] [gmx-user]Error by pdb2gmx
To: gmx-users at gromacs.org

-----------------------------------------------------------
| > Dear Yanmei Song：
> I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command:

There's almost no reason to be using 3.3.1 these days. You'll get much faster performance with 4.0.7

> "pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"
>  
>  I got the error message: 
"  Opening library file ffG45a3.rtp
>   Opening library file  /user/localgromacs/share/gromacs/top/aminoacid.dat
>   Reading min_C16.pdb... 
>  ', 81 atomsin in water
>   Opening library file  /user/localgromacs/share/gromacs/top/xlateat.dat
>   26 out of 26 lines of xlateat.dat converted succesfully
>   Analyzing pdb file
>   There are 1 chains and 0 blocks of water and 1 residues with 81 atoms
> 
>     chain  #res #atoms
>      1 '  '     1     81
>   
>   All occupancies are one
>   Opening library file ffG45a3.atp
>   Atomtype 49
>   Reading residue database... (ffG45a3)
>    Opening library file ffG45a3.rtp
>   Using default: not generating all posible dihedrals
>   Using default:excluding 3 bonded neighbors
>   Using default: generating 1,4 H--H interactions
>  Using default: removing impropers on same bond as a proper
>   -------------------------------------------------------
> >>>> Program pdb2gmx, VERSION 3.3.1
> >>>> Source code file: resall.c, line: 331
> >>>>
> >>>> Fatal error:
> >>>> in .rtp file at line: ">  
> The molecule I added in the ffG45a3.rtp is in attached file

You've clearly broken the .rtp file format, but we can't tell how without seeing the file. Since your attached .rtp file was in some horrible non-text format, I suppose you've probably done something similar when you imported the text into the .rtp file. The .rtp file is plain text, and you want to add plain text.

Mark