[gmx-users] problem with new sugar residue

[Justin A. Lemkul]

Well, what's in the .rtp entry, and what's in your coordinate file?  You 
probably have some inconsistency in your naming that's causing pdb2gmx 
to take issue.

-Justin

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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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