AMBER Archive (2009)

Subject: Re: [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out

From: Rubben Torella (rubben.torella_at_gmail.com)
Date: Tue Oct 06 2009 - 02:56:18 CDT

Hi, have have checked the structures created? with ambpdb -p X.prmtop <
X.lig> try.pdb... check the try.pdb and check, for receptor, complex and
ligand if the structures are correct.
Bye!

2009/10/6 Jeff Yeo <weekiang_at_live.com>

>
> Hi,
>
> I am in the midst of running the binding energy calculations using the
> mm_pbsa.pl script. I checked on the snapshot_com.all.out and found that
> almost all entries have different missing values at different timepoints.
> They either have 'values' of NaN or Infinity or *********.
>
> I doubt this is normal. What may be causing these weird 'values'? The
> generation of snapshots from mdcrd proceeded smoothly and the output file of
> this binding energy calculations did NOT contain any errors or warnings.
>
>
> 156
> BOND = ************* ANGLE = 441946.7100 DIHED =
> 15022.5337
> VDWAALS = ************* EEL = -5029.7507 EGB =
> -20626.4938
> 1-4 VDW = NaN 1-4 EEL = Infinity RESTRAINT =
> 0.0000
>
> 157
> BOND = ************* ANGLE = 465389.2004 DIHED =
> 14791.2394
> VDWAALS = 32227929.3027 EEL = -3444.9296 EGB =
> -21619.6342
> 1-4 VDW = 16964395.6854 1-4 EEL = -2484.8846 RESTRAINT =
> 0.0000
>
> 158
> BOND = ************* ANGLE = 505512.7190 DIHED =
> 14019.5864
> VDWAALS = ************* EEL = -1393.7833 EGB =
> -41493.6393
> 1-4 VDW = ************* 1-4 EEL = -448.3567 RESTRAINT =
> 0.0000
>
>
> 159
> BOND = ************* ANGLE = 512063.7966 DIHED =
> 14958.8929
> VDWAALS = ************* EEL = -1367.3170 EGB =
> -40169.3247
> 1-4 VDW = ************* 1-4 EEL = -183.7412 RESTRAINT =
> 0.0000
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