[gmx-users] atom type not in rtp entry

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 2 04:40:29 CEST 2011

On 2/09/2011 11:47 AM, Sweta Iyer wrote:
> Hi,
> I get the following error message when i try to pdb2gmx my protein file:
> Fatal error:
> Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms
> while sorting atoms.
> I wonder which of these need to be changed!

Please describe your overall simulation objective and copy and paste 
your command line. Not giving them forces us to choose between guessing 
how to help you, or choosing not to do so.

The atom names and residue names in your coordinate file have to be 
matched by pdb2gmx with the contents of the .rtp file. Apparently you 
have a weirdly named atom in a leucine residue. You should be fixing 
your atom and/or residue naming scheme, but without the above 
information, that's all that can be said.


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