Re: [AMBER] Missing values for MM BGAS:error in mm-pbsa

From: <moitrayee.mbu.iisc.ernet.in>
Date: Thu, 25 Mar 2010 12:35:34 +0530 (IST)

No there are no unusual atoms. and the PREFIX is consistent.


> Hi,I have suffered from this problem.First,are there unusual atoms in your
> system,like FŸ
> 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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>
>
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Received on Thu Mar 25 2010 - 01:00:02 PDT
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