[gmx-users] (no subject)

[Yoshus Kumka]

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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