On Mon, Apr 22, 2013, Yongxiu Li wrote:
> 1) ${AMBERHOME}/bin/PropPDB -p x1AHO.pdb -o x12_1AHO.pdb -X 45.9 -Y 40.7
> -Z 30.1 -ix 2 -iy 2 -iz 3
You usually need to construct the unit cell first, then propagate to a
super-cell.
Once you do the "propagation", you must use the supercell parameters
(multiples of the original unit cell parameters) for subsequent operations.
You should of course carefull examine (say in VMD) the resulting pdb files to
make sure you are getting what you want.
> Question2: I do "ambpdb -p solv1AHO.top <solv1AHO.crd
> >solv1AHO1.pdb" and then use vmd to open solv1AHO1.pdb .But I see many
> warning news such as "Warning) Unusual bond between residues: 3192
> (none) and 1342 (waters) " and many water displaying gather together.Why?
If you added lots of waters, many of them may be in bad places until you have
a chance to do careful equilibration. It takes a *lot* of md simulation to
get the waters to be in good places, so plan to keep restraints on the protein
until such equilibration is done.
You might want to solvate waters and minimize a single unit cell first, then
propagate the solvated result to the supercell. It's hard to tell what might
have gone wrong.
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -3.4207E+09 1.5420E+06 8.3886E+06 O 87904
>
> BOND = 188466.4833 ANGLE = 48742.9387 DIHED = 27311.6719
> VDWAALS = ************* EEL = 2893801.6968 HBOND = 0.0000
> 1-4 VDW = 19497.2575 1-4 EEL = 141875.8611 RESTRAINT =
> 0.0000
Try many fewer waters to start with, and see what happens. I'm not clear why
you are getting such bad bond energies, and even extremely high
electrostatics.
...dac
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Received on Thu Apr 25 2013 - 17:00:03 PDT
