This appears to be indicative of a bad mask/topology file definition (note
the error checking in the next version will be worlds better).
Try visualizing the intermediate trajectory files (_MMPBSA_complex.mdcrd,
_MMPBSA_receptor.mdcrd, _MMPBSA_ligand.mdcrd) with their associated
topology files to make sure that they're being created appropriately. (If
they're not, it should be very readily apparent)
HTH,
Jason
On Tue, Nov 8, 2011 at 12:23 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> hi all,
>
> I now have new problems. The MD runs finished fine. I modified the
> ions08.lib file as suggested by Dr. Case. However when I try to perform a
> MMPBSA calculation on the generated trajectories, it never went
> through.(AmberTools 1.5 updated with all the patch files) I see all these
> huge clashes in the _MMPBSA_***_gb.mdout files, such as:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 3.7213E+16 7.8320E+16 5.1146E+18 HA 3273
>
> BOND = 23438545.8760 ANGLE = 368673.1288 DIHED =
> 14366.0233
> VDWAALS = ************* EEL = 65872.2873 EGB =
> -76922.3045
> 1-4 VDW = ************* 1-4 EEL = -15976.3752 RESTRAINT =
> 0.0000
> ESURF = 116.6306
>
>
> TDC 20-> 110 0.000 ********* -35.821 30.160 -47.364
> TDC 21-> 3 0.000 -0.006 7.620 -7.734 0.000
> TDC 21-> 20 0.000 52439.487 41.109 -29.840 -119.690
> TDC 21-> 21 0.000 ********* 25.121 -55.899 515.825
>
>
> However the md output files looks fine. And I did generate receptor, ligand
> etc param files with the modified library. I'm not sure Mg is the cause
> here though I really can't think of anything else. I did the same
> calculation without the mg but with Na as counterions only. And everything
> worked fine.
>
> So how can I fix this? Thanks a lot.
>
>
> Victor
>
>
>
> On Tue, Nov 1, 2011 at 1:09 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
>
> > Plan A worked fine. Thanks a lot, Dr. Case.
> >
> > Victor
> >
> >
> > On Tue, Nov 1, 2011 at 10:51 AM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Tue, Nov 01, 2011, Victor Ma wrote:
> >> >
> >> > I'm running AMBER on a cluster and I have no authority to change the
> >> > $AMBERHOME/dat/leap/lib files. So is there an easy way to do it
> locally?
> >>
> >> Copy everything in $AMBERHOME/dat/leap to some local directory you have
> >> control over. Then, when you load ions8.lib, point specifically to the
> >> local
> >> copy you have changed.
> >>
> >> Or: copy everything under $AMBERHOME to your local directory, set your
> >> AMBERHOME variable to point to the new location, and recompile all the
> >> programs. This has the advantage that Amber is now under *your*
> control,
> >> but
> >> you may have a learning curve as well.
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 08 2011 - 21:00:03 PST
