Hi, amber users.
I am using amber7 to do a mm_pbsa calculation. I ran into problem when I
tried to create coordinates from MD trajector file. The error message is from
the mm_pbsa.log file is:
***********************************************************
=>> Creating coordinates
Executing makecrd
Something wrong with NGR 4421 4420
************************************************************
In my system, total # of atom is 31192. Total # of receptor atom is 4420 and
total # of ligand atom is 54 (from 4421 to 4474).
I used amber6 for the same trajector file and can generate coordinates. I
wandor why it is not work for amber7. Also, would you please let me know what
NGR in the above mm_pbsa.log file stands for.
My mm_pbsa.log file is in below.
#########################################################################
=>> Init data
Presuming executables of amber suite to be in /disk11/amber7/exe
=>> Reading input parameters
Found PREFIX => 1_watcap
Found PATH => ./snapshots/
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => /disk11/wentaofu/mm-pbsa/1_watcap/parm_complex.top
Found RECPT => /disk11/wentaofu/mm-pbsa/1_watcap/parm_protein.top
Found LIGPT => /disk11/wentaofu/mm-pbsa/1_watcap/parm_ligand.top
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found BOX => NO
Found NTOTAL => 31192
Found NSTART => 1
Found NSTOP => 99999
Found NFREQ => 50
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 4421
Found LSTOP => 4474
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 4420
Found FOCUS => 0
Found INDI => 1.0
Found EXDI => 80.0
Found PERFIL => 80.0
Found SCALE => 2
Found LINIT => 1000
Found BNDCON => 4
Found CHARGE => /disk11/wentaofu/mm-pbsa/1_watcap/amber94_delphi.crg
Found SIZE => /disk11/wentaofu/mm-pbsa/1_watcap/parseres.siz
Found SURFTEN => 0.00542
Found SURFOFF => 0.092
Found IGB => 4
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 1.4
Found RADII => /disk11/wentaofu/mm-pbsa/1_watcap/atmtypenumbers
Found TRAJECTORY => ./md05.trj
Found DELPHI => /disk7/lbin/delphi_acad/export/delphi
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
Checking MM
Checking DELPHI
Checking GB
Checking MS
=>> Creating input
Sander input
Delphi input
make_crd input
=>> Creating coordinates
Executing makecrd
Something wrong with NGR 4421 4420
###################################################################
Thanks
Wentao Fu
Center for Pharm. Biotech.
University of Illinois at Chicago
Received on Tue Jan 07 2003 - 16:17:08 PST
