Hi,I have suffered from this problem.First,are there unusual atoms in your system,like F？
second,I see that in this step you set up PREFIX to 2zni,does it consistent with the setting of generating snapshots
> -----Original E-mail-----
> From: moitrayee.mbu.iisc.ernet.in
> Sent Time: 2010-3-25 2:53:26
> To: amber.ambermd.org
> Cc:
> Subject: [AMBER] Missing values for MM BGAS:error in mm-pbsa
>
> Dear Amber users,
>
> I am getting the following error when running pairwise residuewise decomposition
> using mm-pbsa.
> Missing values for MM BGAS
> I am also attaching the relevant pdb file. I have tried what was suggested in
> the previous posts regarding LIGRES/LIGPRI but still getting the error.
> Any suggestions will be of immense help.
> I am pasting below the input for pairwise residuewise decomposition using mm-pbsa.
>
> PREFIX 2zni
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT comp.prm.top
> RECPT rec.prm.top
> LIGPT lig.prm.top
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> ################################################################################
> .DECOMP
> #
> # Energy decomposition parameters (this section is only relevant if DC = 1 above)
> #
> # Energy decomposition is performed for gasphase energies, desolvation free #
> energies calculated with GB, and nonpolar contributions to desolvation #
> using the LCPO method.
> # For amino acids, decomposition is also performed with respect to backbone #
> and sidechain atoms.
> #
> # DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue basis, #
> values of 3 or 4 yield a decomposition on a pairwise per-residue #
> basis. For the latter, so far the number of pairs must not #
> exceed the number of residues in the molecule considered. # Values
> 1 or 3 add 1-4 interactions to bond contributions. # Values 2 or 4
> add 1-4 interactions to either electrostatic or vdW #
> contributions.
> #
> # COMREC - Residues belonging to the receptor molecule IN THE COMPLEX. #
> COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX. # RECRES -
> Residues in the receptor molecule.
> # LIGRES - Residues in the ligand molecule.
> # {COM,REC,LIG}PRI - Residues considered for output.
> # {REC,LIG}MAP - Residues in the complex which are equivalent to the residues
> # in the receptor molecule or the ligand molecule. #
> DCTYPE 4
> #
> COMREC 1-278 280-629 631-702
> COMLIG 279-279 630-630
> COMPRI 1-702
> RECRES 1-278 280-629 631-702
> RECPRI 1-278 280-629 631-702
> RECMAP 1-278 280-629 631-702
> LIGRES 1-2
> LIGPRI 1-2
> LIGMAP 279-279 630-630
> #
> ################################################################################
> .MM
> #
> # MM parameters (this section is only relevant if MM = 1 above)
> #
> # The following parameters are passed to sander.
> # For further details see the sander documentation.
> #
> # DIELC - Dielectricity constant for electrostatic interactions. #
> Note: This is not related to GB calculations.
> #
> DIELC 1.0
> #
> ################################################################################
> .GB
> #
> # GB parameters (this section is only relevant if GB = 1 above)
> #
> # The first group of the following parameters are passed to sander. # For
> further details see the sander documentation.
> #
> # IGB - Switches between Tsui's GB (1), Onufriev's GB (2, 5).
> # GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc. #
> Decomposition only works with ICOSA.
> # SALTCON - Concentration (in M) of 1-1 mobile counterions in solution. #
> EXTDIEL - Dielectricity constant for the solvent.
> # INTDIEL - Dielectricity constant for the solute
> #
> # SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
> # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
> #
> IGB 2
> GBSA 2
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> ################################################################################
> .PROGRAMS
> #
> # Program executables
> #
> DELPHI /home/gohlke/src/delphi.98/exe/delphi
> #
> ################################################################################
>
> Thanks and Regards,
> Moitrayee
>
>
>
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Received on Wed Mar 24 2010 - 18:30:03 PDT
