[gmx-users] problem with new sugar residue

[Tsjerk Wassenaar]

Hi Carmen,

You really have to be careful to match the .rtp to the .pdb building
block. pdb2gmx indicates that there's an atom in the .pdb file, which
is not found in the [ CHIT ] entry in the .rtp file. If you want
better help, you'll have to ask a better question: you should provide
more details regarding the CHIT residue in the .pdb file and the
(relevant part of) the entry in the .rtp file (in this case the [
atoms ] section).

Cheers,

Tsjerk

On Wed, Jun 18, 2008 at 7:29 PM,  <cesteban at unsl.edu.ar> wrote:
> I added a new sugar residue in ffG53a6.rtp file, and I included in  the
> aminaocid.dat file. I got the following problem using pdb2gmx :
> ...................................................................
> Program pdb2gmx, VERSION 3.3.2
> Source code file: pdb2gmx.c, line: 421
>
> Fatal error:
> Atom O in residue CHIT 1 not found in rtp entry with 14 atoms
>             while sorting atoms
> .....................................................................
>
> I solved the problem temporarily changing the name of my new sugar residue
> to "GLCB", that already existed in the ffG53a6.rtp file.
> The question is: How should we do this process with more generality? Are
> there another file which should be modified or edited?
> Thanks a lot
> Carmen Esteban
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623