[gmx-users] rtp entry

[Mark Abraham]

ASHWINI JAYAPRAKASH wrote:
> Hi,
>  
> I am a new gromacs user and have problems creating a topology file using 
> the pdb2gmx command for simulating a six helix bundled alamethecin in 
> lipid bilayer.
> when I use the command :
> pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top
>  
> I get the error :
>  
> Program pdb2gmx, VERSION 3.3.1
> Source code file: pdb2gmx.c, line: 393
> Fatal error:
> Atom CA in residue ACE 1 not found in rtp entry with 6 atoms
>              while sorting atoms

This means what it says. pdb2gmx is finding a CA atom in an ACE residue 
in your coordinate file that it can't reconcile with the .rtp entry for 
ACE for the force field you're using. If this doesn't make any sense, 
you should read chapter five of the manual thoroughly. Probably the 
first four chapters are also worth reading too.

Mark