AMBER Archive (2009)

Subject: Re: [AMBER] Re: MM_PBSA error

From: Ray Luo (ray.luo_at_uci.edu)
Date: Sat Nov 28 2009 - 12:07:26 CST

Your output file shows that you have run it many times. Please clean up
the working folder completely before rerunning MMPBSA again.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Jagdeesh C wrote:
> Hi Mengjuei,
>
> I have pasted and attached my snapshot_com.all.out file. I am not able to
> judge if there is anything wrong with it. Am I overlooking anything? Also
> attached is the log file
>
> Jagdeesh
>
> MM
> GB
> PB
> MS
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> GB_SURFTEN 0.0072
> GB_SURFOFF 0.00
> 1
> 1
> 1
> 1
> 1
> 1
> 1
> BOND = 212.3114 ANGLE = 420.7743 DIHED =
> 503.0257
> VDWAALS = -406.1855 EEL = 1777.1190 EGB =
> -4644.5336
> 1-4 VDW = 191.4888 1-4 EEL = -1800.6156 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8026.754389
> surface area = 4101.096
> ECAVITY = 4101.096
> EDISPER = 0.0000
> 2
> BOND = 201.6401 ANGLE = 426.8700 DIHED =
> 504.1891
> VDWAALS = -412.2048 EEL = 1765.1712 EGB =
> -4603.3917
> 1-4 VDW = 198.7895 1-4 EEL = -1831.1279 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8249.161618
> surface area = 4192.076
> ECAVITY = 4192.076
> EDISPER = 0.0000
> ----------------------------------------------
> ---------------------------------
> --------------------------------
> 7
> BOND = 220.5672 ANGLE = 413.9260 DIHED =
> 482.5076
> VDWAALS = -404.4307 EEL = 1806.9417 EGB =
> -4663.0361
> 1-4 VDW = 192.2423 1-4 EEL = -1798.4127 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8059.801481
> surface area = 4254.963
> ECAVITY = 4254.963
> EDISPER = 0.0000
> 8
> BOND = 178.5407 ANGLE = 407.3751 DIHED =
> 506.9717
> VDWAALS = -389.0358 EEL = 1823.0144 EGB =
> -4678.4791
> 1-4 VDW = 194.9106 1-4 EEL = -1795.4682 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8093.803568
> surface area = 4293.052
> ECAVITY = 4293.052
> EDISPER = 0.0000
> 9
> BOND = 193.7411 ANGLE = 387.9140 DIHED =
> 491.9951
> VDWAALS = -388.4913 EEL = 1794.7958 EGB =
> -4657.8646
> 1-4 VDW = 201.6251 1-4 EEL = -1795.5765 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8124.809823
> surface area = 4363.289
> ECAVITY = 4363.289
> EDISPER = 0.0000
> 10
> BOND = 189.1515 ANGLE = 430.5523 DIHED =
> 487.1259
> VDWAALS = -377.9887 EEL = 1812.7042 EGB =
> -4679.3291
> 1-4 VDW = 198.0546 1-4 EEL = -1825.4908 RESTRAINT =
> 0.0000
> corrected reaction field energy: -8073.202124
> surface area = 4396.153
> ECAVITY = 4396.153
> EDISPER = 0.0000
>
>
>
>
> On Fri, Nov 27, 2009 at 3:09 PM, Mengjuei Hsieh <mjhsieh_at_gmail.com> wrote:
>
>
>> Hi Jagdeesh,
>>
>> You probably need to check the output files in the backward order to
>> see what goes wrong. For example, what is inside the file
>> snapshot_com.all.out?
>>
>> Best,
>> --
>> Mengjuei
>>
>>
>> On Fri, Nov 27, 2009 at 1:20 AM, Jagdeesh C <jagc666_at_gmail.com> wrote:
>>
>>> Hello,
>>> I got this warning in my binding_energy.log
>>> Can someone suggest me what this error might mean. I will give more
>>> information if required.
>>> Thanks
>>> Jagdeesh
>>>
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