AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa does not terminate

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Wed Nov 01 2006 - 11:56:28 CST

I was wondering if the problem could be that I don't have delphi installed. Is this necessary?

Holly Freedman 

--
Department of Physics, University of Alberta
Edmonton CANADA

> Dear AMBER help list,
> 
> I am running mm_pbsa on a trajectory using the input file pasted below.  
> Unfortunately the job seems to never end, and produces an enormous output file 
> (mymm_pbsad01.log).  In this output file, the message 
> 
>     No values for MM_ELE existing -> Skipping
>     Processing PB PBTOT
>         Doing 1 PB PBSOL
>         Doing 1 MM GAS
> 
> is repeated over and over again in what seems like a never-ending loop.
> 
> Can someone please advise me on this problem?
> 
> Thanks in advance,
> Holly Freedman
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
> 
> #
> # Input parameters for mm_pbsa.pl
> #
> # Holger Gohlke
> # 08.01.2002
> #
> 
##############################################################################
> ##
> @GENERAL
> #
> # General parameters
> #   0: means NO; >0: means YES
> #
> #   mm_pbsa allows to calculate (absolute) free energies for one molecular
> #     species or a free energy difference according to:
> #
> #     Receptor + Ligand = Complex, 
> #     DeltaG = G(Complex) - G(Receptor) - G(Ligand).
> #
> #   PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during 
> #            generation of snapshots as well as during mm_pbsa calculations.
> #   PATH - Specifies the location where to store or get snapshots.
> #
> #   COMPLEX - Set to 1 if free energy difference is calculated.
> #   RECEPTOR - Set to 1 if either (absolute) free energy or free energy
> #              difference are calculated.
> #   LIGAND - Set to 1 if free energy difference is calculated.
> #
> #   COMPT - parmtop file for the complex (not necessary for option GC).
> #   RECPT - parmtop file for the receptor (not necessary for option GC).
> #   LIGPT - parmtop file for the ligand (not necessary for option GC).
> #
> #   GC - Snapshots are generated from trajectories (see below).
> #   AS - Residues are mutated during generation of snapshots from trajectories.
> #   DC - Decompose the free energies into individual contributions 
> #        (only works with MM and GB).
> #
> #   MM - Calculation of gas phase energies using sander.
> #   GB - Calculation of desolvation free energies using the GB models in sander
> #        (see below).
> #   PB - Calculation of desolvation free energies using delphi (see below).
> #   MS - Calculation of nonpolar contributions to desolvation using molsurf
> #        (see below).
> #        If MS == 0, nonpolar contributions are calculated with the LCPO method
> #        in sander.
> #   NM - Calculation of entropies with nmode.
> #
> PREFIX                d01
> PATH                  ./
> #
> COMPLEX               0
> RECEPTOR              1
> LIGAND                0
> #
> COMPT                 XXX
> RECPT                 ../../myleapdir/d01.top
> LIGPT                 XXX
> #
> GC                    1
> AS                    0
> DC                    0
> #
> MM                    0 
> GB                    1
> PB                    1
> MS                    1
> #
> NM                    0
> #
> 
##############################################################################
> ##
> @PB
> #
> # PB parameters (this section is only relevant if PB = 1 above)
> #
> #   The following parameters are passed to the PB solver.
> #   Additional parameters (e.g. SALT) may be added here.
> #   For further details see the delphi and pbsa documentation.
> #
> #   PROC - Determines which method is used for solving the PB equation:
> #          If PROC = 1, the delphi program is applied. If PROC = 2,
> #           the pbsa program of the AMBER suite is used.
> #   REFE - Determines which reference state is taken for PB calc:
> #          If REFE = 0, reaction field energy is calculated with EXDI/INDI.
> #            Here, INDI must agree with DIELC from MM part.
> #          If REFE > 0 && INDI > 1.0, the difference of total energies for
> #            combinations EXDI,INDI and 1.0,INDI is calculated.
> #            The electrostatic contribution is NOT taken from sander here.
> #   INDI - Dielectric constant for the molecule.
> #   EXDI - Dielectric constant for the surrounding solvent.
> #   SCALE - Lattice spacing in no. of grids per Angstrom.
> #   LINIT - No. of iterations with linear PB equation.
> #   PRBRAD - Solvent probe radius in A (e.g. use 1.4 with the PARSE parameter se
> t
> #     and 1.6 with the radii optimized by R. Luo)
> #
> #   Parameters for pbsa only
> #
> #   RADIOPT - Option to set up atomic avity radii for molecular surface calculat
> ion
> #     and dielectric assignment. A value of 0 uses the cavity radii from the prm
> top file.
> #     A value of 1 sets up optimized cavity radii at the pbsa initialization pha
> se.
> #     The latter radii are optimized for model compounds of proteins only; use c
> autions
> #     when applying these radii to nucleic acids.
> #
> #   Parameters for delphi only
> #
> #   FOCUS - If FOCUS > 0, subsequent (multiple) PERFIL and SCALE parameters are
> #     used for multiple delphi calculations using the focussing technique.
> #     The # of _focussing_ delphi calculations thus equals the value of FOCUS.
> #   PERFIL - Percentage of the lattice that the largest linear dimension of the
> #            molecule will fill.
> #   CHARGE - Name of the charge file.
> #   SIZE - Name of the size (radii) file.
> #
> #   SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to
> #                  the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
> #
> #
> PROC                  2
> REFE                  0
> INDI                  1.0
> EXDI                  80.0
> SCALE                 2.0
> LINIT                 500
> PRBRAD                1.6
> #
> RADIOPT               0
> #
> FOCUS                 0
> PERFIL                80.0
> CHARGE                ./my_amber94_delphi.crg
> SIZE                  ./my_parse_delphi.siz
> #
> SURFTEN               0.005
> SURFOFF               0.0
> #
> 
##############################################################################
> ##
> @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                  1
> SALTCON               0.00
> EXTDIEL               80.0
> INTDIEL               1.0
> #
> SURFTEN               0.0072
> SURFOFF               0.00
> #
> 
##############################################################################
> ##
> @MS
> #
> # Molsurf parameters (this section is only relevant if MS = 1 above)
> #
> #   PROBE - Radius of the probe sphere used to calculate the SAS.
> #           Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
> #
> PROBE                 0.0
> #
> 
##############################################################################
> ##
> @MAKECRD
> #
> # The following parameters are passed to make_crd_hg, which extracts snapshots
> #   from trajectory files. (This section is only relevant if GC = 1 OR AS = 1 ab
> ove.)
> #
> #   BOX - "YES" means that periodic boundary conditions were used during MD 
> #         simulation and that box information has been printed in the
> #         trajecotry files; "NO" means opposite.
> #   NTOTAL - Total number of atoms per snapshot printed in the trajectory file
> #             (including water, ions, ...).
> #   NSTART - Start structure extraction from NSTART snapshot.
> #   NSTOP - Stop structure extraction at NSTOP snapshot.
> #   NFREQ - Every NFREQ structure will be extracted from the trajectory.
> #
> #   NUMBER_LIG_GROUPS - Number of subsequent LSTART/LSTOP combinations to
> #                       extract atoms belonging to the ligand.
> #   LSTART - Number of first ligand atom in the trajectory entry.
> #   LSTOP - Number of last ligand atom in the trajectory entry.      
> #   NUMBER_REC_GROUPS - Number of subsequent RSTART/RSTOP combinations to
> #                       extract atoms belonging to the receptor.
> #   RSTART - Number of first receptor atom in the trajectory entry.
> #   RSTOP - Number of last receptor atom in the trajectory entry.      
> #   Note: If only one molecular species is extracted, use only the receptor
> #         parameters (NUMBER_REC_GROUPS, RSTART, RSTOP).
> #   
> BOX                   YES
> NTOTAL                51
> NSTART                1
> NSTOP                 300
> NFREQ                 100
> #
> NUMBER_LIG_GROUPS     0
> #LSTART                52
> #LSTOP                 54
> NUMBER_REC_GROUPS     1
> RSTART                1
> RSTOP                 51
> #
> 
##############################################################################
> ##
> #
> @TRAJECTORY
> #
> # Trajectory names
> #
> #   The following trajectories are used to extract snapshots with "make_crd_hg":
> #   Each trajectory name must be preceeded by the TRAJECTORY card.
> #   Subsequent trajectories are considered together; trajectories may be 
> #     in ascii as well as in .gz format. 
> #   To be able to identify the title line, it must be identical in all files. 
> #
> TRAJECTORY            ../../d01/strip.traj
> #
> 
##############################################################################
> ##
> #
> @PROGRAMS
> #
> # Program executables
> #
> #DELPHI                /home/gohlke/src/delphi.98/exe/delphi
> #
> 
##############################################################################
> ##
>  
> 
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu