Most likely the files were generated wrong, can you properly visualize
all the water-free files in VMD?
Ray
On Tue, May 8, 2012 at 8:56 AM, 21119012 <21119012.zju.edu.cn> wrote:
> Hi Bill,
>
> Thank you for your reply. The problem has just been resolved.
>
> In general namelist variables of MMPBSA.py, "strip_mask" means the variable that specifies which atoms are stripped from the trajectory. Default = ":WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+". That is, MG2 will be removed from trajectory by MMPBSA.py when trajin initial mdrcd file for later energy calculation.
>
> There is a MG2 in my system which is stripped out by PTRAJ so the produced mdcrd files become inconsistent with the corresponding prmtop files. This is the reason for my case.
>
> Solution: add the following to the "mmpbsa.in" file:
> strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
> You may find MG2 is not included here.
>
> Thanks again.
>
> Cao Yang,
> Zhejiang University, China
>
>
>
>>From: Bill Miller III <brmilleriii.gmail.com>
>>Reply-To: AMBER Mailing List <amber.ambermd.org>
>>To: xiaojiong <xiaojiong.zju.edu.cn>,AMBER Mailing List <amber.ambermd.org>
>>Subject: Re: [AMBER] high value in MMPBSA
>>Date: Tue, 8 May 2012 07:51:08 -0400
>>
>>As the error message suggests, there appears to be inconsistencies with the parameters among your different topology files. I would suggest recreating your dry complex, receptor, and ligand prmtops from your solvated complex prmtop using ante-MMPBSA.py or parmed.py.
>>
>>
>>I hope that helps.
>>
>>-Bill
>>
>>
>>
>>On May 8, 2012, at 5:34 AM, "xiaojiong"
> wrote:
>>
>>> Hi,
>>>
>>> I came across a problem in MMPBSA calculation recently. The binding free energy is extremely high especially for the VDWAALS and 1-4 VDW part.
>>> I examine the "_MMPBSA_complex.pdb" file in VMD and find that the structure of the ligand crushes while the amino acids are OK.
>>> I guess there are some inconsistencies between the prmtop file and the trajectories of the ligand. But I couldn't figure out the point. Could you give me some suggestions?
>>>
>>> Here is the "FINAL_RESULTS_MMPBSA.dat" file:
>>>
>>> |Input file:
>>> |--------------------------------------------------------------
>>> |Input file for running PB and GB
>>> |&general
>>> | startframe=201, verbose=1,
>>> |# entropy=1,
>>> |/
>>> |&gb
>>> | igb=2, saltcon=0.100
>>> |/
>>> |&pb
>>> | istrng=0.100,
>>> |/
>>> |
>>> |
>>> |--------------------------------------------------------------
>>> |Solvated complex topology file: 3BWY_neg_lut5_LYN_SAM.prmtop
>>> |Complex topology file: 3BWY_neg_lut5_LYN_SAM_nosolv.prmtop
>>> |Receptor topology file: 3BWY_neg_lut5_LYN_SAM_noH_nolut.prmtop
>>> |Ligand topology file: neg_luteolin5.prmtop
>>> |Initial mdcrd(s): production3.mdcrd
>>> |
>>> |Best guess for receptor mask: ":1-216"
>>> |Best guess for ligand mask: ":217"
>>> |Ligand residue name is "LUT"
>>> |
>>> |Calculations performed using 200 frames.
>>> |Poisson Boltzmann calculations performed using internal PBSA solver in sander.
>>> |
>>> |All units are reported in kcal/mole.
>>> -------------------------------------------------------------------------------
>>> -------------------------------------------------------------------------------
>>>
>>> GENERALIZED BORN:
>>>
>>>
>>>
>>> WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
>>> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
>>>
>>> The most common cause of this is inconsistent charge definitions across topology files.
>>> Complex:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 21006150336550031360.0000 212017833520375070720.0000 15029545730918023168.0000
>>> EEL -7468.4040 1236.3948 87.6457
>>> 1-4 VDW 4282229701684408877056.0000 42099142055861577318400.0000 2984329055037626515456.0000
>>> 1-4 EEL 982.2488 968.2529 68.6376
>>> EGB -5610.6208 465.7548 33.0165
>>> ESURF 55.2802 2.3492 0.1665
>>>
>>> G gas 4303235852020958101504.0000 42097542547851609899008.0000 2984215668921074188288.0000
>>> G solv -5555.3406 465.9751 33.0321
>>>
>>> TOTAL 4303235852020958101504.0000 42097542547851609899008.0000 2984215668921074188288.0000
>>>
>>>
>>> Receptor:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 21005544796506038272.0000 212017893069718487040.0000 15029549952259053568.0000
>>> EEL -7695.4620 1235.8941 87.6102
>>> 1-4 VDW 4281985119177865691136.0000 42099166792161559576576.0000 2984330808547440328704.0000
>>> 1-4 EEL 1443.2652 958.3304 67.9342
>>> EGB -5608.2873 478.6512 33.9307
>>> ESURF 55.9342 2.4598 0.1744
>>>
>>> G gas 4302990663974364119040.0000 42097567469026228043776.0000 2984217435536303325184.0000
>>> G solv -5552.3531 478.9203 33.9498
>>>
>>> TOTAL 4302990663974364119040.0000 42097567469026228043776.0000 2984217435536303325184.0000
>>>
>>>
>>> Ligand:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 141210847715258.3125 1666571428388523.0000 118140116238851.9688
>>> EEL 252.6849 97.0809 6.8819
>>> 1-4 VDW 244582506544392416.0000 3440575681575656960.0000 243895943507772832.0000
>>> 1-4 EEL -461.0165 83.8380 5.9431
>>> EGB -164.6754 30.2935 2.1475
>>> ESURF 2.6234 0.2556 0.0181
>>>
>>> G gas 244723717392107936.0000 3440566046845218816.0000 243895260519840544.0000
>>> G solv -162.0521 30.3183 2.1492
>>>
>>> TOTAL 244723717392107904.0000 3440566046845219328.0000 243895260519840576.0000
>>>
>>>
>>> Differences (Complex - Receptor - Ligand):
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 464329196269944.4375 6456047927338494.0000 457657103432328.0625
>>> EEL -25.6269 102.8246 7.2890
>>> 1-4 VDW -488.0288 4686.7461 332.2346
>>> 1-4 EEL -0.0000 0.0001 0.0000
>>> EGB 162.3420 79.1399 5.6101
>>> ESURF -3.2774 0.9013 0.0639
>>>
>>> DELTA G gas 464329196191104.1875 6456047927344164.0000 457657103432730.0000
>>> DELTA G solv 159.0645 79.0900 5.6065
>>>
>>>
>>> DELTA G binding = 464329196191261.6875 +/- 6456047927344175.0000 457657103432730.8125
>>>
>>>
>>> -------------------------------------------------------------------------------
>>> -------------------------------------------------------------------------------
>>>
>>> POISSON BOLTZMANN:
>>>
>>>
>>>
>>> WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
>>> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check differences)!
>>>
>>> The most common cause of this is inconsistent charge definitions across topology files.
>>> Complex:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 21006150336550055936.0000 212017833520375234560.0000 15029545730918033408.0000
>>> EEL -7468.4040 1236.3948 87.6457
>>> 1-4 VDW 4282229701684408877056.0000 42099142055861577318400.0000 2984329055037626515456.0000
>>> 1-4 EEL 982.2488 968.2529 68.6376
>>> EPB -4320.4560 369.9319 26.2238
>>> ECAVITY 53.0443 0.8530 0.0605
>>>
>>> G gas 4303235852020958101504.0000 42097542547851609899008.0000 2984215668921074188288.0000
>>> G solv -4267.4117 369.6239 26.2019
>>>
>>> TOTAL 4303235852020958101504.0000 42097542547851609899008.0000 2984215668921074188288.0000
>>>
>>>
>>> Receptor:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 21005544796506054656.0000 212017893069718683648.0000 15029549952259067904.0000
>>> EEL -7695.4620 1235.8941 87.6102
>>> 1-4 VDW 4281985119177865691136.0000 42099166792161559576576.0000 2984330808547440328704.0000
>>> 1-4 EEL 1443.2652 958.3304 67.9342
>>> EPB -4348.3379 384.4561 27.2534
>>> ECAVITY 53.2268 0.8828 0.0626
>>>
>>> G gas 4302990663974364119040.0000 42097567469026228043776.0000 2984217435536303325184.0000
>>> G solv -4295.1110 384.1966 27.2350
>>>
>>> TOTAL 4302990663974364119040.0000 42097567469026228043776.0000 2984217435536303325184.0000
>>>
>>>
>>> Ligand:
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 141210847715258.4062 1666571428388523.7500 118140116238852.0312
>>> EEL 252.6849 97.0809 6.8819
>>> 1-4 VDW 244582506544392416.0000 3440575681575656960.0000 243895943507772832.0000
>>> 1-4 EEL -461.0165 83.8380 5.9431
>>> EPB -143.9965 26.3195 1.8657
>>> ECAVITY 1.8704 0.3239 0.0230
>>>
>>> G gas 244723717392107936.0000 3440566046845218816.0000 243895260519840544.0000
>>> G solv -142.1260 26.3208 1.8658
>>>
>>> TOTAL 244723717392107904.0000 3440566046845219328.0000 243895260519840576.0000
>>>
>>>
>>> Differences (Complex - Receptor - Ligand):
>>> Energy Component Average Std. Dev. Std. Err. of Mean
>>> -------------------------------------------------------------------------------
>>> VDWAALS 464329196269953.1875 6456047927338652.0000 457657103432339.3125
>>> EEL -25.6269 102.8246 7.2890
>>> 1-4 VDW -488.0288 4686.7461 332.2346
>>> 1-4 EEL -0.0000 0.0001 0.0000
>>> EPB 171.8783 85.5514 6.0646
>>> ECAVITY -2.0530 0.3528 0.0250
>>>
>>> DELTA G gas 464329196191114.7500 6456047927344320.0000 457657103432741.0625
>>> DELTA G solv 169.8253 85.5208 6.0624
>>>
>>>
>>> DELTA G binding = 464329196191280.3750 +/- 6456047927344334.0000 457657103432742.0625
>>>
>>>
>>> -------------------------------------------------------------------------------
>>> -------------------------------------------------------------------------------
>>>
>>> Cao Yang,
>>> Zhejiang University, China
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue May 08 2012 - 10:00:04 PDT
