AMBER Archive (2007)

Subject: AMBER: (no subject)

From: n.buis_at_soton.ac.uk
Date: Thu Jul 19 2007 - 03:58:06 CDT

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

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