Hello,
I am trying to a simple energy minimization with my DNA
molecule I created with 3DNA program. Below is a snippet of a pdb file where
I've only included coordinates for one residue to save space (Actual file
contains coordinates for 12-mer DNA).
So my question is why is the pdb2gmx spitting out Fatal Error: Atom P in
residue DG 0 not found in rtp entry entry DGN with 32 atoms while sorting
atoms? I am using forcefield94 and looking at the .rtp file and atom P is
surely present in the forcefield. Is the pdb format? Something else?
If it the format then does anyone know how to properly put together a pdb file
of a nucleic acid and show me what it looks like, and what forcefields are good
for DNA ligand interactions?
thanks in advance
REMARK 3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
ATOM 1 P DG A 1 -0.356 9.218 1.848
ATOM 2 O1P DG A 1 -0.311 10.489 2.605
ATOM 3 O2P DG A 1 -1.334 9.156 0.740
ATOM 4 O5' DG A 1 1.105 8.869 1.295
ATOM 5 C5' DG A 1 2.021 8.156 2.146
ATOM 6 C4' DG A 1 2.726 7.072 1.355
ATOM 7 O4' DG A 1 1.986 5.817 1.352
ATOM 8 C3' DG A 1 2.952 7.370 -0.127
ATOM 9 O3' DG A 1 4.210 6.832 -0.518
ATOM 10 C2' DG A 1 1.848 6.598 -0.850
ATOM 11 C1' DG A 1 1.913 5.344 0.016
ATOM 12 N9 DG A 1 0.711 4.472 -0.101
ATOM 13 C8 DG A 1 -0.606 4.826 -0.294
ATOM 14 N7 DG A 1 -1.430 3.807 -0.354
ATOM 15 C5 DG A 1 -0.599 2.700 -0.190
ATOM 16 C6 DG A 1 -0.914 1.317 -0.165
ATOM 17 O6 DG A 1 -2.010 0.775 -0.284
ATOM 18 N1 DG A 1 0.233 0.533 0.025
ATOM 19 C2 DG A 1 1.516 1.023 0.172
ATOM 20 N2 DG A 1 2.476 0.111 0.344
ATOM 21 N3 DG A 1 1.811 2.321 0.149
ATOM 22 C4 DG A 1 0.709 3.095 -0.035
END
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