Hello,
> Hello everyone,
>
> I am trying to get binding energy of a mutated protein with its ligand. After test of mm-pbsa in the Examples, I test it with my own system with mm-pbsa, but always get into trouble and no Bond Vdwaals and 1-4VDW values is given out.
>
> I have check the *prmtop and change different mdcrd to test. But still can not overcome the problem. I have checked the output pdb for the complex when doing pbsa. And the mdcrd is a final 1ns dcd of a 30ns namd dcd file transformed by amber ptraj.
>
> If it is the problem with prmtop, do you have any suggestions on checking it effectively? If not, do you have any suggestions on improving it.
> The output is as follows:
>
> output of MM-GBSA
> #####################################################################################
> pro-lig_com.all.out
> MM
> GB
> MS
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> GB_SURFTEN 0.0072
> GB_SURFOFF 0.00
> 1
> BOND = 874.7425 ANGLE = 2539.0853 DIHED = 3470.6028
> VDWAALS = -2411.0741 EEL = -19336.7814 EGB = -3540.2770
> 1-4 VDW = 1216.8740 1-4 EEL = 11839.6272 RESTRAINT = 0.0000
> surface area = 18310.2767
The first frame here appears to be correct -- you have what seem to be
reasonable numbers for the terms
> 2
> BOND = 10804824.1381 ANGLE = 469191.8854 DIHED = 16271.5596
> VDWAALS = ************* EEL = -16973.2372 EGB = -6318.0368
> 1-4 VDW = ************* 1-4 EEL = 9154.1513 RESTRAINT = 0.0000
> surface area = 15517.4713
All of these numbers (except for, perhaps, EEL) seem very wrong.
Bond, angle, and dihedral values are orders of magnitude greater than
they were in the previous frame, which clearly cannot be correct.
This suggests that the topology files are inconsistent with the
trajectory file. All future frames have the same problem as frame 2
> 3
> BOND = 13204617.2939 ANGLE = 418026.7166 DIHED = 17233.2463
> VDWAALS = ************* EEL = -9439.1589 EGB = -6246.3031
> 1-4 VDW = ************* 1-4 EEL = 1566.7690 RESTRAINT = 0.0000
> surface area = 14823.5458
> 4
> BOND = 14003168.0315 ANGLE = 367093.8707 DIHED = 15489.5072
> VDWAALS = 17656579.3728 EEL = -5403.4655 EGB = -6671.6425
> 1-4 VDW = 12584392.5139 1-4 EEL = -3236.4822 RESTRAINT = 0.0000
> surface area = 14913.0201
> ################################################################################
> for ligand
> 1
> BOND = 13.8815 ANGLE = 59.7811 DIHED = 10.7636
> VDWAALS = -4.5483 EEL = 57.7862 EGB = -31.8879
> 1-4 VDW = 14.7125 1-4 EEL = -148.0538 RESTRAINT = 0.0000
> surface area = 437.9018
The fact that the first frame appears correct leads me to believe that
it is, that is that the coordinate file has extra atoms (waters?
counterions? etc.). Thus, the second frame will be using solvent
coordinates as solute coordinates, giving rise to these ridiculous
numbers. Ultimately, however, the prmtops and mdcrds are
incompatible. If the problem is that solvent is still present in the
mdcrd when it shouldn't be, use ptraj to strip the unnecessary atoms
from the mdcrd.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 14 2010 - 08:30:01 PST
