AMBER Archive (2009)

Subject: Re: [AMBER] Re: MM_PBSA error

From: Jagdeesh C (jagc666_at_gmail.com)
Date: Fri Nov 27 2009 - 04:13:36 CST

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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>




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