On Mon, May 24, 2010, Nicee wrote:
>
> I am trying to minimize a protein which has aspartate, po4, glycerol
> , Nadp and water in pdb file. I have generated prepin and frcmod file
> for all of the above from antechamber as per tutorial and loaded them
> in tleap and saved the prmtop and inpcrd file, but on miminizing the
> protein for 500 steps the minimization stops at 230 step and gives the
> following error :
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 230 -2.2468E+04 1.2248E+04 9.9638E+05 O3P 5114
>
> BOND = 358.4270 ANGLE = 826.4138 DIHED = 3289.6600
> VDWAALS = -2513.4377 EEL = -25000.7354 HBOND = 0.0000
> 1-4 VDW = 1148.6144 1-4 EEL = -577.0991 RESTRAINT = 0.0000
> Frac coord min, max: -0.338855902014186 1.12539885977885
>
>
> Frac coord min, max: -0.338855902014186 1.12539885977885
> The system has extended beyond
> the extent of the virtual box.
> ntb=0,
> cut=10
You are asking for a vacuum simulation of a highly polar system, which is
likely to have high forces and be unstable. My guess is that you will
need to solvate your system, and run it as a periodic system.
>
> I tried run a similar minimization with maxcyc=230 and the
> .out and .restrt file were generated. Then i generated pdb
> (new7_mtb3_min12_pdb.pdb) for this restrt file and visualized it in
> pdb. The O3P and H22 atom appeared to be overlapped.
Problems like this are not uncommon for phosphate-containing systems. It is
possible (likely?) that the H22 atom has zero Lennard-Jones parameters, which
may need to be fixed.
....dac
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Received on Mon May 24 2010 - 06:00:17 PDT
