AMBER Archive (2007)

Subject: AMBER: follow-up

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Fri Sep 28 2007 - 14:55:39 CDT

When I create the pdb file by ambpdb, I got the
following message?

 ambpdb -p G.top < G.ann.x > g_md.pdb

| New format PARM file being parsed.
| Version = 1.000 Date = 09/18/07 Time = 23:12:25
At line 624 of file _ambpdb.f (Unit 5)
Traceback: not available, compile with -ftrace=frame
or -ftrace=full
Fortran runtime error: Bad value during floating point
read

Could you please give me some help for this ?

Wenyong

--- Wenyong Tong <wenyong_tong_at_yahoo.com> wrote:

> Hello, David
>
> Thank you for suggestions.
>
> (1) I only input part of distance restrains because
> MD
> just stopped if given all of restrains. I guessed
> some
> of assignments were not right.
> (2) It seems that the format of my “anneal.in” file
> had some problems.
> (3) I run a short time annealing with new .in files.
> Result seems ok. Any suggestions for this?
>
===============================================================================
>
> KE Trans = 0.0000 KE Rot = 0.0000
> C.O.M. Vel = 0.000000
>
> Translational and rotational motion removed
>
> KE Trans = 0.0000 KE Rot = 0.0000
> C.O.M. Vel = 0.000000
>
> NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K)
> =
> 24.27 PRESS = 0.0
> Etot = -114.4606 EKtot = 10.6366
> EPtot = -125.0971
> BOND = 15.5273 ANGLE = 34.3019
> DIHED = -35.8702
> 1-4 NB = 32.3989 1-4 EEL = 1137.2888
> VDWAALS = -48.6193
> EELEC = -760.3267 EGB = -499.8236
> RESTRAINT = 0.0258
> EAMBER (non-restraint) = -125.1229
>
>
------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.026 Angle = 0.000
>
> Torsion = 0.000
>
===============================================================================
>
> A V E R A G E S O V E R 550000 S T E P S
>
>
> NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K)
> =
> 909.62 PRESS = 0.0
> Etot = 458.2530 EKtot = 398.5732
> EPtot = 59.6798
> BOND = 59.2379 ANGLE = 133.2183
> DIHED = -15.3631
> 1-4 NB = 38.7507 1-4 EEL = 1129.0126
> VDWAALS = -40.8537
> EELEC = -732.1089 EGB = -512.7310
> RESTRAINT = 0.5171
> EAMBER (non-restraint) = 59.1627
>
>
------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.026 Angle = 0.000
>
> Torsion = 0.000
>
===============================================================================
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 550000 TIME(PS) = 1100.000 TEMP(K)
> =
> 228.70 PRESS = 0.0
> Etot = 139.8929 EKtot = 100.2091
> EPtot = 43.2414
> BOND = 12.9421 ANGLE = 24.8968
> DIHED = 5.8055
> 1-4 NB = 3.7961 1-4 EEL = 16.8955
> VDWAALS = 3.8772
> EELEC = 23.5680 EGB = 16.1573
> RESTRAINT = 0.7451
> EAMBER (non-restraint) = 42.4962
>
>
------------------------------------------------------------------------------
>
>
>
>
>
> --- "David A. Case" <case_at_scripps.edu> wrote:
>
> > On Wed, Sep 26, 2007, Wenyong Tong wrote:
> > >
> > > Could you please give some suggestions about the
> > > following results from NMR refinement? Please
> note
> > > that the final temperature did not get down.
> >
> > You should examine the beginning of the input
> file,
> > where the program prints
> > out the weight change information: be sure it
> seems
> > to do what you want.
> >
> > I don't see anything obviously wrong with the
> input,
> > but I'm probably missing
> > something. But try some short(!) test cases to
> make
> > sure annealing is doing
> > what you want -- something like 1,000 to 10,000
> > times shorter than what you
> > showed here.
> >
> > >
> > > NMR restraints: Bond = 0.045 Angle =
> > 0.000
> > > Torsion = 0.000
> >
> > Note that even without cooling, you have
> essentially
> > zero restraint
> > violations. I have no idea whether this means
> that
> > your structures are really
> > good, or that your restraints are too weak, but it
> > is something to look into.
> >
> > ...dac
> >
> >
>
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> >
>
> Wenyong
>
>
>
>
>
>
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