[gmx-users] Atom CA used in that entry is not found in the input file

[Justin Lemkul]

On 4/26/20 4:45 PM, Daniel Burns wrote:
> Hello,
>
> I edited a few selenomethionine residues, changing "S" to "SD" and removed
> the "SE" at the end of the line.  I then ran pdb2gmx with Charmm36.  I get
> the following error (not sure why the residue number doesn't match):
>
> Fatal error:
> Residue 324 named GLY of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> My .pdb file section looks like this:
> ATOM    569  N   MET A 324      87.364  46.446  53.851  1.00  3.42
>    N
> ATOM    570  CA  MET A 324      86.617  45.972  52.679  1.00  6.50
>    C
> ATOM    571  C   MET A 324      87.405  46.212  51.424  1.00  6.43
>    C
> ATOM    572  O   MET A 324      86.987  45.830  50.332  1.00  8.80
>    O
> ATOM    573  CB  MET A 324      85.203  46.573  52.584  1.00  5.66
>    C
> ATOM    574  CG  MET A 324      84.258  46.053  53.663  1.00  5.50
>    C
> ATOM    575  CE  MET A 324      83.200  44.225  51.772  1.00  3.19
>    C
> ATOM    576  SD  MET A 324      83.876  44.132  53.563  1.00 14.27
>    S
> ATOM    577  N   GLY A 325      88.553  46.854  51.604  1.00  9.51
>    N
> ATOM    578  CA  GLY A 325      89.548  47.012  50.546  1.00  9.78
>    C
> ATOM    579  C   GLY A 325      89.087  47.608  49.227  1.00  9.91
>    C
> ATOM    580  O   GLY A 325      89.352  47.048  48.159  1.00 11.43
>    O
> ATOM    581  N   GLY A 326      88.403  48.742  49.271  1.00  7.35
>    N
> ATOM    582  CA  GLY A 326      87.942  49.290  48.005  1.00  6.34
>    C
> ATOM    583  C   GLY A 326      86.542  48.875  47.602  1.00  3.91
>    C
> ATOM    584  O   GLY A 326      85.947  49.547  46.765  1.00  4.00
>    O
>
> I don't see anything wrong with my GLY residues and none of the other
> Glycines are presenting an error.  This does follow one of my edited MET
> residues.

Please provide the full screen output from pdb2gmx.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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