[gmx-developers] gromacs can't recognize residue name with four letters in some cases

Dongsheng Zhang dong at pampas.chem.purdue.edu
Sat Aug 5 16:33:02 CEST 2006

Dear XAvier,

Thank you for reply!

On Sat, 2006-08-05 at 11:18 +0200, X.Periole wrote:
> > In my pdb file, some residues' names have four letters. 
> >When I use
> > pdb2gmx, it works fine. The output gro file shows those 
> >residues (with
> > four letters). When I use editconf -f *gro -o *pdb, 
> >gromacs can't
> > recognize those residues with four letters. All 
> >residues' names in the
> > output pdb file have only three letters. For those 
> >residues whose name
> > have four letters, the last letter has been truncated. 
> >Please check it.
> Why do they have four letters names ? Are they 
> unconventional
> residues ? 

Yes. They are unconventional. In fact, I have seen some residues whose
names have four letters at http://www.pdb.org
> If no you should be able to change their name
> via a script or by hand with a text editor. 

Sure. I can do that. It is a little bit inconvenient. I think it is
better that gromacs can recognize it as the command pdb2gmx.

> In the case of
> unconventional residues you should check weather they are
> defined in the topology ffXXX.rtp and modify the names.

I have defined my own rtp file. It is fine.
> XAvier
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list