Yoshus Kumka wrote:
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?
The problem is that you have a 5' phosphate, which the .rtp file does not
expect. The error message is saying that it found a P atom in the .pdb file,
but that atom is not present in the .rtp entry.
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?
There have been some discussions in the past about how to properly build
termini; check the list archive. The choice of force field is not problematic,
but the agreement between the structure and the expectations of that force field is.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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