AMBER Archive (2006)

Subject: RE: AMBER: molsurf.c error

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Thu May 04 2006 - 14:43:41 CDT

Thanks Dr. Walker! You were right. I did not recompile correctly mm_pbsa
after changing the MAXAT value on molsurf.h.
However I am still getting the error: “molsurf: molsurf.c:1055: is_buried:
Assertion `sarg1 >= 0.0' failed”. Has anyone experienced this problem
before?
The unsolvated pdb files used to create the top files for the complex,
protein and ligand were derived from the solvated pdb file obtained from the
initial top and coordinate files. Besides strip the water and ions is it
necessary to do something else?

Any suggestions would be appreciated.

Thanks
Miguel

>From: "Ross Walker" <ross_at_rosswalker.co.uk>
>Reply-To: amber_at_scripps.edu
>To: <amber_at_scripps.edu>
>Subject: RE: AMBER: molsurf.c error
>Date: Thu, 4 May 2006 09:28:49 -0700
>
>Dear Miguel,
>
>How many atoms does your system actually have? Is it more than 10000?
>
>Also the error message you show still reports MAXAT=10000 exceeded. What
>did
>you change the value of MAXAT in molsurf.h to?
>
>I suspect that you did not recompile mm_pbsa after changing the value. Make
>sure you cd to $AMBERHOME/src/mm_pbsa
>
>then do:
>
>make clean
>
>make
>make install
>
>This will copy over the new executable into $AMBERHOME/exe/
>
>double check this by looking at the date on the file.
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Miguel Ferreira
> > Sent: Thursday, May 04, 2006 09:01
> > To: amber_at_scripps.edu
> > Subject: AMBER: molsurf.c error
> >
> > Hi all,
> >
> >
> > I am still with problems with mm_pbsa calculations. The error is the
> > following:
> >
> > -- > MAXAT=10000 exceeded
> > molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
> > Use of uninitialized value in multiplication (*) at
> > /scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
> > Use of uninitialized value in multiplication (*) at
> > /scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
> > Use of uninitialized value in multiplication (*) at
> > /scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
> > No data for 0+0 MS SURF 0
> >
> > [1] Exit 134 mm_pbsa.pl mm.pbsa.in >
> > mm.pbsa.out
> >
> >
> > As I previously increased the variable MAXAT in molsurf.c
> > file (as said in
> > http://amber.ch.ic.ac.uk/archive/200404/0370.html), I
> > don´t understand the reason of this error. Should I change the MAXAT
> > variable in another file?
> > Does anyone know what the error with molsurf.c:1055 means and
> > how to solve
> > this problem?
> > I think my input files are ok. I created pdb files from the
> > unsolvated top
> > files and they look normal.
> > Here is mm_pbsa.out:
> >
> >
> > =>> Init data
> > Presuming executables of amber suite to be in /scratch/amber8/exe
> >
> > =>> Reading input parameters
> > Found PREFIX => complex
> > Found PATH => ./
> > Found COMPLEX => 1
> > Found RECEPTOR => 1
> > Found LIGAND => 1
> > Found COMPT => ./complex.top
> > Found RECPT => ./protein.top
> > Found LIGPT => ./ligand.top
> > Found GC => 1
> > Found AS => 0
> > Found DC => 0
> > Found MM => 1
> > Found GB => 0
> > Found PB => 1
> > Found MS => 1
> > Found NM => 0
> > Found PROC => 2
> > Found REFE => 0
> > Found INDI => 1.0
> > Found EXDI => 80.0
> > Found SCALE => 2.5
> > Found LINIT => 1000
> > Found MAXC => 0.001
> > Found PRBRAD => 1.4
> > Found RADIOPT => 0
> > Found FOCUS => 0
> > Found PERFIL => 80.0
> > Found CHARGE => ./complex.crg
> > Found SIZE => ./my_parse_delphi.siz
> > Found SURFTEN => 0.005
> > Found SURFOFF => 0.0
> > Found DIELC => 1.0
> > Found PROBE => 0.0
> > Found BOX => NO
> > Found NTOTAL => 15504
> > Found NSTART => 0
> > Found NSTOP => 1
> > Found NFREQ => 1
> > Found NUMBER_LIG_GROUPS => 4
> > Found LSTART => 15041
> > Found LSTOP => 15156
> > Found LSTART => 15157
> > Found LSTOP => 15272
> > Found LSTART => 15273
> > Found LSTOP => 15388
> > Found LSTART => 15389
> > Found LSTOP => 15504
> > Found NUMBER_REC_GROUPS => 4
> > Found RSTART => 1
> > Found RSTOP => 3760
> > Found RSTART => 3761
> > Found RSTOP => 7520
> > Found RSTART => 7521
> > Found RSTOP => 11280
> > Found RSTART => 11281
> > Found RSTOP => 15040
> > Found TRAJECTORY => ./complex.trj
> >
> > =>> Checking sanity
> > Checking GENERAL
> > Checking GC
> > Checking TRAJ
> > Checking MM
> > Checking PB
> > Checking MS
> >
> > =>> Creating input
> > Sander input
> > PBSA input
> > make_crd input
> >
> > =>> Creating coordinates
> > Executing makecrd
> >
> > Amber8 Module: make_crg_hg
> >
> > usage: make_crd_hg < trajectory_file
> >
> >
> > =>> Calculating energy / entropy contributions
> > Calc contrib for ./complex _com.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > Calc MS
> > Calc contrib for ./complex _rec.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > Calc MS
> > Calc contrib for ./complex _lig.crd.1
> > Calc MM/GB/SAS
> > Generate PDB
> > Center PDB
> > Calc PBSA
> > Generate PQR
> > Calc MS
> >
> > =>> Doing statistics
> > =>> Values of global variables
> > TEMP = 300
> > R = 8.314
> > gammaP = 0.005
> > betaP = 0.0
> > gammaG = 0.0072
> > betaG = 0
> > =>> Reading input
> > =>> Reordering files
> > Final order:
> > 1. complex _com.all.out: -
> > 2. complex _rec.all.out: -
> > 3. complex _lig.all.out: -
> > =>> Reading files
> > Reading complex _com.all.out
> > WARNING: Missing SURF for MS in 0 -> Taken from -1
> > Reading complex _rec.all.out
> > Checking CALC
> > WARNING: Missing SURF for MS in 0 -> Taken from -1
> > Reading complex _lig.all.out
> > Checking CALC
> > WARNING: Missing SURF for MS in 0 -> Taken from -1
> > =>> Treat special parameters
> > =>> Calc missing parameters
> > Processing MM GAS
> > Doing 1 MM ELE
> > No values for MM_ELE existing -> Skipping
> > Processing MM INT
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Processing MM ELE
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Processing MM VDW
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Processing PB PBSOL
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Processing PB PBELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Processing PB PBTOT
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > No values for MM_GAS existing -> Skipping
> > Processing MM GAS
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Processing PB PBTOT
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > =>> Calc delta from raw data
> >
> >
> > Thanks in advance!
> > Miguel
> >
> > --------------------------------------------------------------
> > ---------
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> >
>
>
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