Dear Dr. Sgro,
Responding on your recent e-mail message to Willem Melchers
regarding the modeling of the 3'-NTR of enteroviral RNA,
and your kind offer to put the video on CD-ROM.
About the modeling, I have built the models using SYBYL 6.0
and the AMBER all atom ff. I'm pretty sure that the version
implemented at that time was AMBER 3.0A. For the initial
model, I used very very moderate conditions (just trying
to find a viable conformation), like 8 Angstrom non-bonded
cutoff, library charges, no solvent, no counterions, etc.
RMS gradient < 0.05 kcal/mol/A^2. We were actually quite happy
about those first results, but soon it started to itch, and I
started up dynamics runs to find better (energetically AND
geometrically) conformations. I switched to MacroModel/Batchmin
(version 5.0) and the AMBER* ff. Extended non-bonded cutoffs
to 8 and 20 Angstrom for VdW, respectively electrostatics,
included the GB/SA solvent model to mimic solvation and
reoptimized until the RMS gradient was less than 0.025 kJ/mol/A^2.
Other settings as recommended in the MacroModel documentation.
The MD runs were performed using the same conditions and
all bonds constrained using SHAKE, timestep 1 fs, explicit regeneration
of the non-bonded array every ps, thermal batch to scale velocities,
initial heating from 0 to 300 K in 3 ps, followed by five 200 ps
runs, sampling every 10 ps. Each of the intermediate results
was 'frozen' by 18ps runs to cool to 30K and were subsequently
minimized until the RMS gradient was less than 0.05 kJ/mol/A^2.
Calculation were performed on the SGI Challenge L on a single
R10000 processor taking up roughly 1200 hours cpu time (measured
on a uninterrupted system...).
I'm writing things up right now for publication, although
I haven't decided on the journal. Any suggestions ?
Regarding the video, I don't know whether you've seen it, cause
I heard from Willem that there were some technical problems
showing during the meeting. The video was created from animated
gifs, compiled into so-called .fli files. Perhaps they are
more suitable to prepare cd-roms with QT movies...?
Just let me know if you're interested.
Looking forward to hear your comments on the calculations.
With best regards,
Hilbert Bruins
Last Modified September 30, 1999