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

[Per Larsson]

If atoms are missing in the sidechains of your protein, you can try a  
program like scwrl3 to rebuild all or some of the sidechains. This  
will give you complete sidechains in sort of reasonable positions.

Cheers
/Per




12 aug 2008 kl. 15.04 skrev vivek sharma:

> Hi David,
> Thanx a lot again. can you please tell me the criteria or the  
> standards to do such correction or can you suggest some link or  
> tutorial for the same?
> whether swiss pdb can help in such cases?
>
> With Thanx,
> Vivek
>
>
>
> 2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se>
> 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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