AMBER Archive (2003)

Subject: mm_pbsa question

From: wentaofu (wentaofu_at_uic.edu)
Date: Tue Jan 07 2003 - 18:17:08 CST

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