[gmx-users] hi

[Mark Abraham]

Moutusi Manna wrote:
>          I want to perform simulation of transmembrane
> peptide. I have a perseuillibrated POPO (hydrated)
> bilayer (using CHARMM),containing more than 32,000
> atom. But when I try to convert ".pdb" to ".gro" using
> "pdb2gmx", it shows the following error

The role of pdb2gmx is not convert a .pdb to a .gro, it is to generate a 
topology file from a structure file. It outputs a structure file that is 
consistent with that topology file, but that structure file can be in 
several formats. See pdb2gmx -h.

> Fatal error:
> Residue "popc" not found in residue topology detabase
> 
> Please suggest how I can overcome this problem .

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

If this makes no sense (and even if it does) reading relevant parts of 
chapter 5 of the GROMACS manual will be needed here.

Mark