[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[David van der Spoel]

vivek sharma wrote:
> Hi There,
>
> I am new to molecular dynamics and GROMACS.
> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the 
> command....
>
>  pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite 
> hydrogen -water spce
>
> I got the following in the last of error.....
> ......
> ......
> ......
> .......
> N-terminus: NH3+
> C-terminus: COO-
> WARNING: atom CE2 not found in residue 270 while adding atom
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: genhydro.c, line: 304
>
> Fatal error:
> Atom CE2 not found in residue PHE270 while adding hydrogens
> -------------------------------------------------------
>  I tried the same with different force field and water models, but 
> getting the same error again and again.
> any suggestion will be highly appreciated.

You have an incorrect pdb file. An atom is missing. You have to fix it 
yourself.
>
>
> With thanx,
> Vivek
>
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>
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