[gmx-users] problem with new sugar residue

[Tsjerk Wassenaar]

Hi Carmen,

Well, adding a residue to aminoacids.dat only makes sense for amino
acids (although I admit to fiddle it sometimes, in which case it is
usually best to make a local copy). But one thing with amino acids is
that backbone -N(H)-Ca-C(O)- thing, which is referred to in the
termini database. I guess that was what was bothering yo. You could
check by running pdb2gmx with -ter and select none for the
carbohydrate chain. Another possibility is that you didn't have chain
identifiers (or TER statements) in the pdb file, which made pdb2gmx
think to deal with a single chain in which an amino acid should be
attached to the foregoing residue (carbohydrate), referring to some
atom "O" on that residue which would then be needed to get the
dihedral definitions right. But that is speculation... It would still
help everybody if you would (in the future) provide more information.
You're still not telling anything informative.

Tsjerk

On Thu, Jun 19, 2008 at 10:39 PM,  <cesteban at unsl.edu.ar> wrote:
> Many thanks in advance,but the problem seems to be solved just by not
> including the new residue name in the aminoacids.dat file, despite the
> instruction to do so in sec.5.5.1 chapter 5 Topologies of the manual.
> Can you tell me if this procedure is correct?
> Thanks again
> Carmen
>> 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
>> _______________________________________________
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>
>
>
>
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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