I just ran into this problem and found out that it was occurring due to
incorrect numbering of the crd files. I noticed that in the output file,
the "=>> Calculating energy / entropy contributions" section was empty,
which means that the energies were never computed, thus the "Missing MM BGAS
values" error (all the values are actually missing). When run correctly,
the section should look like this:
=>> Calculating energy / entropy contributions
Calc contrib for ../snaps/RCL_DGP_com.crd.1
Calc MM/GB/SAS
Calc contrib for ../snaps/RCL_DGP_com.crd.2
Calc MM/GB/SAS
...
So, i my case, i was trying to use a group of crd files that i had selected
from a large set of outputs. My crd files began with PREFIX_com.crd.10000,
but it seem that the way the mm_pbsa.pl script is written, it will search
your PATH directory for PREFIX_com.crd.1 first, and if it doesn't find that
file, then no output will be generated, and you will receive the Missing
Values error. Once i renamed the crd files to start with .1, things ran
correctly. Hope this helps,
ryan
On Sun, Aug 16, 2009 at 2:49 PM, Maria Mirza <maryamirza.gmail.com> wrote:
> Hello,
>
> I saw this message a while back on the AMBER mailing list. I am trying to
> do
> something similar to you with a drug + receptor complex and getting the
> same
> error of "Missing MM BGAS values". I am wondering if you were able to
> resolve this?
>
> regards
> Maria
>
> On Mon, Apr 6, 2009 at 10:35 AM, Lucilla Angeli <angeli10.unisi.it> wrote:
>
> > Dear amber users,
> >
> > I have problem on running mmpbsa using AMBER10 to obtain the decompose
> > energy. I have extracted 700 snapshots and then I'm trying to perform
> > the decompose_energy.in as show below; I found the error during the
> > mmpbsa process like this
> >
> > "Missing values for MM BGAS"
> >
> > My decompose_energy.in file is the following:
> >
> > .GENERAL
> > PREFIX a_decomp
> > PATH ./
> > #
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > #
> > COMPT ../prot-lig.prmtop
> > RECPT ../prot.prmtop
> > LIGPT ../lig.prmtop
> > #
> > GC 0
> > AS 0
> > DC 1
> > #
> > MM 1
> > GB 1
> > PB 0
> > MS 0
> > #
> > NM 0
> > #
> >
> >
> ################################################################################
> > .DECOMP
> > DCTYPE 2
> > #
> > COMREC 1-265,267
> > COMLIG 266-266
> > COMPRI 1-265 266-266
> > RECRES 1-265,267
> > RECPRI 1-265,267
> > RECMAP 1-265,267
> > LIGRES 1-1
> > LIGPRI 1-1
> > LIGMAP 266-266
> > #
> >
> >
> ################################################################################
> > .MM
> >
> > DIELC 1.0
> > #
> >
> >
> ################################################################################
> > .GB
> > IGB 2
> > GBSA 2
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > #
> > SURFTEN 0.0072
> > SURFOFF 0.00
> >
> > Since in my protein there are zinc atoms I have modified the
> > file /amber10/src/mm_pbsa/mm_pbsa_calceneent.pm with the Zinc
> > parameters, but without success. The problem remains.
> >
> > Any suggestions will be grate.
> >
> > Thank you in advance,
> >
> >
> >
> >
> > *********************************
> > Dr.Lucilla Angeli
> > Dip. Farmaco Chimico Tecnologico
> > Universita' degli Studi Di Siena
> > Via Aldo Moro
> > I-53100 Siena, Italy
> > Phone: ++39 0577 234256
> > Fax: ++39 0577 234333
> > e-mail angeli10.unisi.it
> > **********************************
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Only 'No Differences' can make a difference.
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>
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Received on Fri Feb 19 2010 - 12:00:02 PST
