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
