Hi Mark,
Thank you for your valuable suggestion.I did go through the manual, but I
want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, and if
so I am not sure what the appropiate Type of angles, Type of proper dihedrals,
Type of improper dihedrals I have to enter.
If I choose the force field with option 0 then it gives me an error saying
residue AIB not found in residue topology.
Any help would be highly appreciated.
Thanks,
Aj
Mark Abraham <[EMAIL PROTECTED]> wrote:
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.
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