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 - 09:00:03 PDT
