On Mon, 2015-02-23 at 15:36 +0330, Fatemeh Sadat Alavi wrote:
> when I run minimization step, I look at the structure, with help VMD to
> visualize complex_solvated.pdb and complex_solvated_min2.pdb
> ( ambpdb -p complex_solvated.prmtop < complex_solvated.inpcrd >
> complex_solvated.pdb
> ambpdb -p complex_solvated.prmtop < min2.rst > complex_solvated_min2.pdb )
You can visualize the prmtop and incprd files directly with VMD... no
need to create a PDB file. See
http://ambermd.org/tutorials/basic/tutorial2/
>
> I compared the starting structure and the minimized structure. I can see the
> the structure has changed slightly, and I think that there are no major
> problem.
> If I don't have good minimized structure, What do I do? How do I understand
> it?
Look at the maximum gradient in the output file of the minimization. It
looks something like this:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.1262E+03 2.2137E+01 1.2322E+02 CA 1102
BOND = 631.8993 ANGLE = 898.2543 DIHED = 566.4453
VDWAALS = -768.3629 EEL = -7874.4913 EGB = -1943.0838
1-4 VDW = 348.8246 1-4 EEL = 5980.5047 RESTRAINT = 0.0000
ESURF = 33.8338
In this case, GMAX is 123.22 kcal/mol/A. A large gradient means large
forces that will blow up your system.
If your minimized structure is not minimized enough, either you did not
run a long enough minimization or your system cannot be satisfactorily
minimized (for instance, if your box dimensions are wrong).
> As I said before, I calculated MD (heating) with ntwx=1 ntpr=1 ntslim=100 ,I
> saw heat.mdcrd and complex_solvated.prmtop files by chimera software!
> When I use ptraj comment, I can't show RMSD of diagram because I have zero
> for all.
> I use this script (rmsd.in) :
> "trajin heat.mdcrd
> reference min2.rst
> rms reference out RMSD.rms "
> and then I run;
> ptraj complex_solvated.prmtop < rmsd.in
>
> please give your valuable comment.
I'll suggest what I suggested last time: use cpptraj to see if there are
any particle overlaps between periodic images of your particles. See my
last email for how to do that.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 23 2015 - 05:30:02 PST
