Hi, I'm trying to reproduce a structure of a nucleic acid (RNA in this case). I built an RNA helix using W. Olson's 3X3DNA, calculated the distances and implemented them as restraints in xplor. (PDB validation gives no errors on angles and bond-lengths, and NOE backcalculation gives no violation for a severely overdetermined system).
When I run a POWEL or short verlet dynamics the structure runs away from the perfect conformation (only potentials included are: noe bonds vdw angles, impropers) I see a huge increase in energy of the bonds and angles, while the structure is initially in it's energy minimum. I checked the topology and parameter files: topallhdg.dna and parallhdg.dna They contain the wrong values for bondlengths and angles. Meaning, they do not match Olson's model (which is correct according to pdb validation-software from rcbs.org, and also according to the references: JACS (1996), vol.118 iss. 3, pp. 509-518 JACS (1996), vol.118 iss. 3, pp. 519-529 An example: O4'-C4' and O4'-C1' have the same length, whereas they should be 1.453 and 1.414 respectively. Is there another topology file I can use for this purpose? Are these 'mistakes' made on purpose (with a physical idea behind it), or is it actually wrong ? Regards, Ramon
