[gmx-users] (no subject)

[Justin A. Lemkul]

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
> 

-- 
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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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