[gmx-users] Missing H from residue

[Justin A. Lemkul]

Jack Shultz wrote:

<snip>

> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pdb2gmx.c, line: 429
> 
> Fatal error:
> Atom O in residue CARG 244 not found in rtp entry with 25 atoms
>              while sorting atoms
> -------------------------------------------------------
> 
> But we got an O here
> ATOM   3822  O   CARG  153      -4.455 -21.080   2.791  1.00  0.00           O
> 

The error is not telling you that the O atom is missing from the .pdb file; it 
is telling you that it is present in the .pdb, but not in the .rtp entry.  Look 
at the .rtp entry for CARG - you should have an O1 and O2 atom for the 
C-terminal carboxylate.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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