Dear amber users
I am facing problems when trying to run MM-PBSA, with ALA_SCANNING switched
on. I have run the example MM_PBSA files on the ras_raf_II_wt system and
have these working correctly for my system, however when I turn the
ALA_SCANNING switch on, I receive the following message.
/usr/local/amber9//exe/sander -O -i sander_com.in -o sander_com.1.out -c
./ras_raf_II_wt_com.crd.1 -p ./ras_raf_II_wt.prmtop not successful
The log file output.
=>> Init data
Presuming executables of amber suite to be in /usr/local/amber9//exe
=>> Reading input parameters
Found PREFIX => ras_raf_II_wt
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./ras_raf_II_wt.prmtop
Found RECPT => ./ras_II_wt.prmtop
Found LIGPT => ./raf_wt.prmtop
Found GC => 1
Found AS => 1
Found DC => 0
Found MM => 1
Found GB => 1
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
Found LINIT => 1000
Found PRBRAD => 1.4
Found ISTRNG => 0.0
Found RADIOPT => 0
Found NPOPT => 1
Found CAVITY_SURFTEN => 0.0072
Found CAVITY_OFFSET => 0.00
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
Found DIELC => 4
Found MAXCYC => 10000
Found DRMS => 0.0001
Found BOX => NO
Found NTOTAL => 36606
Found NSTART => 1
Found NSTOP => 5
Found NFREQ => 1
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 2622
Found LSTOP => 3862
Found NUMBER_REC_GROUPS => 2
Found RSTART => 1
Found RSTOP => 2621
Found RSTART => 3863
Found RSTOP => 3907
Found NUMBER_MUTANT_GROUPS => 2
Found MUTANT_ATOM1 => 1480
Found MUTANT_ATOM2 => 0
Found MUTANT_KEEP => 1486
Found MUTANT_REFERENCE => 1477
Found MUTANT_ATOM2 => 1498
Found MUTANT_ATOM1 => 1494
Found MUTANT_KEEP => 1500
Found MUTANT_REFERENCE => 1492
Found TRAJECTORY => ./md_traj_short.mdcrd
=>> Checking sanity
Checking GENERAL
Checking GC
Checking AS
Checking TRAJ
Checking MM
Checking PB
Checking GB
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 ./ras_raf_II_wt_com.crd.1
Calc MM/GB/SAS
I have run the same file with the AS = 0 and have got the binding energy
out, so my questions are, is it possible to perform ALA_SCANNING-MM_PBSA in
this way or do I need to alter the prmtop file for each time I want to run a
new ALA replacement. The second question is " If I mutate 2 residues as in
the input file above, is it possible to print out the binding energy for
the un-mutate, point one mutation and point two mutation separately or will
it carry out both mutations at once ?".
Any comment would be great.
Best regards,
Nick
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Received on Sun Jul 22 2007 - 06:07:27 PDT
