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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

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