Hi,
How do you create your topology and parameters files?
I got the same problem when I used the "combine" command in tleap.
If you did that too, follow D. A. Case advice :
http://archive.ambermd.org/201510/0057.html
Otherwise, please send us the commands that you used in tleap and the
parameter and topology files.
Jérémie Knoops
2015-10-19 23:22 GMT+02:00 Renato Freitas <renatoffs.gmail.com>:
> Hi all,
>
> I ran a 10ns MD simulation (all the topology files were made using the same
> procedures and the same force field) for a protein-ligand complex, and I
> used the MMPBSA.py script to calculate the binding energy. I noted that the
> 1-4 nonbonded interactions do not completely cancel out in the total
> binding free energy, resulting in a large positive value for deltaG.
>
> Can anyone tell me what could be the cause of this error?
>
> Thanks,
>
> Renato
>
>
> | Run on Mon Oct 19 13:00:46 2015
>
> |
>
> |Input file:
>
> |--------------------------------------------------------------
>
> |Input file for running PB and GB
>
> |&general
>
> |startframe=401, endframe=2000, interval=2,
>
> |keep_files=2, verbose=1,
>
> |/
>
> |&gb
>
> | igb=2,
>
> |/
>
> |--------------------------------------------------------------
>
> |MMPBSA.py Version=13.0
>
> |Solvated complex topology file: ../01-topology/p53pb1-MS03-com.prmtop
>
> |Complex topology file: ../01-topology/p53pb1-MS03-com_gas.prmtop
>
> |Receptor topology file: ../01-topology/p53pb1_rec.prmtop
>
> |Ligand topology file: ../01-topology/MS03-lig.prmtop
>
> |Initial mdcrd(s): md.nc
>
> |
>
> |Receptor mask: ":1-242"
>
> |Ligand mask: ":243"
>
> |Ligand residue name is "<0>"
>
> |
>
> |Calculations performed using 800 complex frames.
>
> |
>
> |Generalized Born ESURF calculated using 'LCPO' surface areas
>
> |
>
> |All units are reported in kcal/mole.
>
>
> -------------------------------------------------------------------------------
>
>
> -------------------------------------------------------------------------------
>
>
> GENERALIZED BORN:
>
>
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
>
> TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
>
> Complex:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> -------------------------------------------------------------------------------
>
> BOND 749.9153 22.8509
> 0.8079
>
> ANGLE 1907.7526 34.1289
> 1.2066
>
> DIHED 2353.7020 18.9509
> 0.6700
>
> VDWAALS -1865.8201 22.0098
> 0.7782
>
> EEL -18333.6598 99.9502
> 3.5338
>
> 1-4 VDW 24170.3751 102.8768
> 3.6372
>
> 1-4 EEL 10561.4546 39.4539
> 1.3949
>
> EGB -3029.4324 82.7667
> 2.9262
>
> ESURF 79.4987 1.8955
> 0.0670
>
>
> G gas 19543.7197 140.8169
> 4.9786
>
> G solv -2949.9337 81.7106
> 2.8889
>
>
> TOTAL 16593.7860 111.0293
> 3.9255
>
>
>
> Receptor:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> -------------------------------------------------------------------------------
>
> BOND 740.3852 22.7670
> 0.8049
>
> ANGLE 1880.5317 34.1086
> 1.2059
>
> DIHED 2333.7538 18.8189
> 0.6653
>
> VDWAALS -1828.3004 21.6050
> 0.7639
>
> EEL -18151.7131 104.2307
> 3.6851
>
> 1-4 VDW 868.8332 12.2155
> 0.4319
>
> 1-4 EEL 10547.3401 39.8234
> 1.4080
>
> EGB -3127.9186 86.3691
> 3.0536
>
> ESURF 81.0024 1.8407
> 0.0651
>
>
> G gas -3609.1695 103.0658
> 3.6439
>
> G solv -3046.9161 85.3087
> 3.0161
>
>
> TOTAL -6656.0856 44.5797
> 1.5761
>
>
>
> Ligand:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> -------------------------------------------------------------------------------
>
> BOND 9.5300 2.6855
> 0.0949
>
> ANGLE 27.2209 3.5335
> 0.1249
>
> DIHED 19.9482 2.4322
> 0.0860
>
> VDWAALS -2.1882 1.6912
> 0.0598
>
> EEL -15.6794 3.8096
> 0.1347
>
> 1-4 VDW 1434.5710 6.4096
> 0.2266
>
> 1-4 EEL -159.0709 4.3259
> 0.1529
>
> EGB -70.8238 1.5366
> 0.0543
>
> ESURF 2.9300 0.0156
> 0.0006
>
>
> G gas 1314.3316 7.8732
> 0.2784
>
> G solv -67.8938 1.5334
> 0.0542
>
>
> TOTAL 1246.4378 7.6494
> 0.2704
>
>
>
> Differences (Complex - Receptor - Ligand):
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
>
> -------------------------------------------------------------------------------
>
> BOND -0.0000 0.0000
> 0.0000
>
> ANGLE -0.0000 0.0000
> 0.0000
>
> DIHED -0.0000 0.0000
> 0.0000
>
> VDWAALS -35.3315 2.6688
> 0.0944
>
> EEL -166.2673 13.0078
> 0.4599
>
> 1-4 VDW 21866.9709 101.5898
> 3.5917
>
> 1-4 EEL 173.1854 0.5204
> 0.0184
>
> EGB 169.3100 11.1054
> 0.3926
>
> ESURF -4.4337 0.2677
> 0.0095
>
>
> DELTA G gas 21838.5576 102.8667
> 3.6369
>
> DELTA G solv 164.8763 10.9990
> 0.3889
>
>
> DELTA TOTAL 22003.4338 101.6630
> 3.5943
>
>
>
>
> -------------------------------------------------------------------------------
>
>
> -------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 20 2015 - 01:00:03 PDT
