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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Received on Thu May 04 2006 - 17:10:41 PDT
