Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not
using ffamber if you are running automated tests, since there are quirks with
requiring specific nomenclature (for lysine, histidine, terminal residues, etc).
-Justin
Jack Shultz wrote:
Justin,
Can you suggest any pdb files I could use that are more simple? I've
been trying to use files from tutorials but it seems like are always
problematic.
Jack
On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul <[email protected]> wrote:
Jack Shultz wrote:
Hello,
I just wanted to compare results between single and double precision.
I reused the same parameters. Single works. Double caused errors on
mdrun. Any idea why?
http://hydrogenathome.org/result.php?resultid=1292662
I don't know why any of that worked at all. You've got missing atoms and
inconsistent naming (LYSH should be LYP if you really want a protonated
lysine under the Amber ports, etc). Did you give pdb2gmx -missing?
Otherwise, topology generation should have failed.
Especially troublesome:
System has non-zero total charge: -2.309866e+01
I would suggest running tests on a physically realistic system that has all
atoms present and an integer charge. Maybe single precision somehow
overcame these topology problems, but I wouldn't trust any of the results.
-Justin
-------------------------------------------------------
Program mdrun, VERSION 4.0.3
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 300 ]
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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