[gmx-users] problem with new sugar residue

[cesteban at unsl.edu.ar]

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
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> The Netherlands
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