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:
ATOM569 N MET A 324 87.364 46.446 53.851 1.00 3.42
N
ATOM570 CA MET A 324 86.617 45.972 52.679 1.00 6.50
C
ATOM571 C MET A 324 87.405 46.212 51.424 1.00 6.43
C
ATOM572 O MET A 324 86.987 45.830 50.332 1.00 8.80
O
ATOM573 CB MET A 324 85.203 46.573 52.584 1.00 5.66
C
ATOM574 CG MET A 324 84.258 46.053 53.663 1.00 5.50
C
ATOM575 CE MET A 324 83.200 44.225 51.772 1.00 3.19
C
ATOM576 SD MET A 324 83.876 44.132 53.563 1.00 14.27
S
ATOM577 N GLY A 325 88.553 46.854 51.604 1.00 9.51
N
ATOM578 CA GLY A 325 89.548 47.012 50.546 1.00 9.78
C
ATOM579 C GLY A 325 89.087 47.608 49.227 1.00 9.91
C
ATOM580 O GLY A 325 89.352 47.048 48.159 1.00 11.43
O
ATOM581 N GLY A 326 88.403 48.742 49.271 1.00 7.35
N
ATOM582 CA GLY A 326 87.942 49.290 48.005 1.00 6.34
C
ATOM583 C GLY A 326 86.542 48.875 47.602 1.00 3.91
C
ATOM584 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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