Hi,
I checked the messages shown on the screen :
ptraj found! Using /root/amber11/bin/ptraj
sander found! Using /root/amber9/exe/sander (serial only!)
Assuming /root/amber9/exe/sander is part of
amber9 or amber10. Using old PB input file.
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
Bondi radii (mbondi)
Preparing trajectories with ptraj...
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER trajectory
file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
101 frames were read in and processed by ptraj for use in calculation.
Starting sander calls
Starting gb calculation...
bad atom type: K
bad atom type: K
Starting pb calculation...
Cannot match namelist object name cutcap
namelist read: misplaced = sign
Cannot match namelist object name 1
Cannot match namelist object name xcap
namelist read: misplaced = sign
Cannot match namelist object name ycap
namelist read: misplaced = sign
Cannot match namelist object name zcap
.................................
My system is a quadruplex dna with central K+ ions. I guess K+ ions are not
well defined to treat in GB. However K+ ions are recognized well in amber as
I didn't have any problem in MD runs.
Kindly help.
Thanks a lot..
Asfa.
On Wed, Jun 30, 2010 at 7:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The stuff printed to stderr and stdout should contain your error messages.
> What is actually printed out by MMPBSA.py to the screen? Or to wherever
> stdout and stderr were redirected if that's the case.
>
> All the best,
> Jason
>
> On Wed, Jun 30, 2010 at 9:10 AM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > Take a look at the _MMPBSA_*_gb.mdout and _MMPBSA_*_pb.mdout files. There
> > should be some helpful information in those files.
> >
> > -Bill
> >
> > On Wed, Jun 30, 2010 at 6:47 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I am running MMPBSA.py for the first time. The script I used for
> testing
> > > is:
> > >
> > > Input file for running PB and GB
> > > &general
> > > startframe=5700, endframe=6000, interval=10, verbose=1,
> > > # entropy=1,
> > > /
> > > &gb
> > > igb=2, saltcon=0.100
> > > /
> > > &pb
> > > istrng=0.100,
> > > /
> > >
> > > I am getting all the _MMPBSA* files but in FINAL_RES_MMPBSA.dat, I get
> > only
> > > :
> > >
> > > | Run on Wed Jun 30 16:05:19 IST 2010
> > >
> > > |Input file:
> > > |--------------------------------------------------------------
> > > |Input file for running PB and GB
> > > |&general
> > > | startframe=5700, endframe=6000, interval=10, verbose=1,
> > > |# entropy=1,
> > > |/
> > > |&gb
> > > | igb=2, saltcon=0.100
> > > |/
> > > |&pb
> > > | istrng=0.100,
> > > |/
> > > |
> > > |--------------------------------------------------------------
> > > |Solvated complex topology file: com143d_wat.prmtop
> > > |Complex topology file: com143d_vac.prmtop
> > > |Receptor topology file: 143d_rec_vac.prmtop
> > > |Ligand topology file: lig_vac.prmtop
> > > |Initial mdcrd(s): 143de2K_md2_agn.mdcrd
> > > |
> > > |Best guess for receptor mask: ":1-24"
> > > |Best guess for ligand mask: ":25"
> > > |Ligand residue name is "LIG"
> > > |
> > > |Calculations performed using 31 frames.
> > > |Poisson Boltzmann calculations performed using internal PBSA solver in
> > > sander.
> > > |
> > > |All units are reported in kcal/mole.
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > > No other information is given. Can u plz tell me where am I going
> wrong?
> > >
> > > Thanks a lot..
> > > Asfa.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 30 2010 - 08:00:04 PDT
