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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 23:12:37 PDT
