Hello,
I see a couple of issues with your input. First, by default K+ ions are
stripped from your coordinate file. If you do not remove the K+ ions from
the topology files, then your topology files will not match your coordinate
files (resulting in the ptraj warning you see below:
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
). Second, it's likely that you didn't use GB when you ran your initial MD,
but rather explicit solvent, correct? In this case, K+ may not be able to
be handled by sander when running GB, and you may have to add a parameter
into the source code and recompile. However, K+ is not explicitly key to
binding, then I would recreate topology files without these ions and just
use the saltcon variable.
As for the errors you're getting in PB, I thought our version created an
input file compatible with amber9, but it looks like I was mistaken. You'll
have to go through the input file (in the function pbmdin_old in utils.py)
and adjust it so that it works for sander. I'm guessing you'll have to
remove cutcap, xcap, ycap, and zcap.
Hope this helps,
Jason
On Wed, Jun 30, 2010 at 10:40 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> 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
> >
> _______________________________________________
> 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
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Received on Wed Jun 30 2010 - 08:30:03 PDT
