On 2/25/13 6:09 AM, Group Gro wrote:
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous users in the
previous e-mails, but I have read the answers and suggestions to those posts and I am not
still able to solve the problem based on them. It is completely possible that I am just
not seeing the obvious, so I apologize, but I would welcome any advice. I want to work on
"Human Glutathione Peroxidase" and downloaded its pdb file, but when I try
pdb2gmx, I face Fatal Error:
Program pdb2gmx, VERSION 4.5.5
Source code file:
/build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 91
Fatal error:
Atom CD is used in an interaction of
type atom in the topology
database, but an atom of that name was
not found in residue
number 50.
I tried different force fields, for example OPLS-AA/L all-atom force field,
different versions of AMBERs, but I
always get the same problem! When I tried GROMOS's versions, the problem goes
on CZ atom instead of CD. Here is a chunk of my pdb file (I have also attached
the full pdb file to this e-mail):
SHEET 6 A 1 PHE A 183 PRO A190 0
SHEET 7 A 1 GLY A 192 HIS A200 0
MODEL
ATOM 1 N GLY A 38 -4.242 -9.833 -26.316 1.00 0.00 N
ATOM 2 CA GLY A 38 -3.416 -10.949 -25.765 1.00 0.00 C
ATOM 3 C GLY A 38 -1.953 -10.570 -25.632 1.00 0.00 C
ATOM 4 O GLY A 38 -1.069
-11.266 -26.159 1.00 0.00 O
ATOM 5 N THR A 39 -1.673 -9.461 -24.940 1.00 0.00 N
ATOM 6 CA THR A 39 -0.286 -9.039 -24.705 1.00 0.00 C
ATOM 7 C THR A 39 -0.073 -8.722 -23.214 1.00 0.00 C
ATOM 8 O THR A 39 -1.035 -8.559 -22.442 1.00
0.00 O
ATOM 9 CB THR A 39 0.124 -7.784 -25.533 1.00 0.00 C
ATOM 10 OG1 THR A 39 -0.415 -6.602 -24.926 1.00 0.00 O
ATOM 11 CG2 THR A 39 -0.309 -7.882 -27.037 1.00 0.00 C
…..
ATOM 91 OD1 ASP A 49 10.106 1.841 -5.471 1.00 0.00 O
ATOM 92 OD2 ASP A 49 12.010 2.918 -5.273 1.00 0.00 O
ATOM 93 N GLY A 50 8.192 0.495 -3.643 1.00 0.00 N
ATOM 94 CA GLY A 50 6.805 0.919 -3.449 1.00 0.00 C
ATOM 95 C GLY A 50 6.525 2.278 -4.054 1.00 0.00 C
ATOM
96 O GLY A 50 5.449 2.818 -3.864 1.00 0.00 O
ATOM 97 N GLU A 51 7.471 2.832 -4.802 1.00 0.00 N
ATOM 98 CA GLU A 51 7.351 4.238 -5.211 1.00 0.00 C
ATOM 99 C GLU A 51 6.737 4.438 -6.592 1.00 0.00 C
ATOM 100 O GLU A
51 6.291 5.522 -6.897 1.00 0.00 O
ATOM 101 CB GLU A 51 8.713 4.941 -5.174 1.00 0.00 C
ATOM 102 CG GLU A 51 9.283 5.140 -3.759 1.00 0.00 C
ATOM 103 CD GLU A 51 8.612 6.301 -3.006 1.00 0.00 C
ATOM 104 N GLU A 52 6.729
3.418 -7.432 1.00 0.00 N
….
ATOM 3035 OH TYR A 228 -9.320
-43.377 -52.577 1.00 0.00 O
TER 3036 TYR A 228
ENDMDL
HETATM 3037 CL CL 11000 -16.070
-39.525 -6.168 1.00 0.00 CL
HETATM 3038 NA NA 11001 -1.679
-34.065 -0.491 1.00 0.00 NA
CONECT 996 1519
CONECT 1021 1519
CONECT 1519 996 1021
END
I know that the residue number printed
by pdb2gmx is actually starting from zero, so the problem is actually in GLU.
In both rtp file and pdb I have CD atom. Some suggestions wanted to
change the order of C and O in pdb file, but it didn't work. What should I do?
Your statements are inconsistent. You say above that changing the force field
triggers a problem with a different atom (CZ instead of CD), which doesn't make
much sense. The amino acids have standard atom nomenclature, so changing the
force field should not change the error. Beyond that, the real reason is that
you're missing an atom somewhere and the PDB header should have clearing
"MISSING" lines that tell you exactly what that is. If you need further help
diagnosing, providing the actual PDB code would be helpful.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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