AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA: decompose energy error

From: Maria Mirza (maryamirza_at_gmail.com)
Date: Sun Aug 16 2009 - 14:49:06 CDT


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_at_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_at_unisi.it
> **********************************
>
>
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>

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