AMBER Archive (2006)

Subject: RE: AMBER: molsurf.c error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 04 2006 - 11:28:49 CDT

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

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> -----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
> donīt 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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