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

[Justin A. Lemkul]

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.
> 

Sounds like the crystal structure has missing atoms.  You'll need to reconstruct 
the missing portions with a modeling program like DeepView or Modeller.

-Justin

> 
> With thanx,
> Vivek
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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