AMBER Archive (2004)

Subject: AMBER: error in mm_pbsa

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sat Oct 16 2004 - 04:12:41 CDT

Dear Amber users,

When I run
mm_pbsa.pl mm_pbsa.in >mm_pbsa.log & in Amber7 doing binding energy between protein and ligand

Illegal character in prototype for mm_pbsa_statistics::mm_pbsa_stat : $calc_delta,$calc_dec,$input,$output,$snap_min,$snap_max at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 275.
Illegal character in prototype for mm_pbsa_statistics::output : $output,$calc_delta at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 363.
Illegal character in prototype for mm_pbsa_statistics::output_snap : $output,$calc_delta,$snap_min at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 493.
Using an array as a reference is deprecated at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 560.
.....
.....
.....
Illegal character in prototype for main::read_radii_pattern : $r_mol->{"RADII"},\%unit_rad,\%exp_rad,\@pat at /usr/amber7/exe/mm_pbsa.pl line 1354.
Illegal character in prototype for main::generate_pdb : $pdb,$ncrdfile,$npar,$r_pro at /usr/amber7/exe/mm_pbsa.pl line 1419.
Illegal character in prototype for main::calc_MM_GB_SAS : *OUT,$nsan,$sanout,$ncrdfile,$npar,$r_gen,$r_pro at /usr/amber7/exe/mm_pbsa.pl line 1456.
Illegal character in prototype for main::calc_PB : $OUT,$pdbbase,$outbase,\%DEL,\%PRO at /usr/amber7/exe/mm_pbsa.pl line 1513.
Illegal character in prototype for main::calc_statistics : \%GEN,\%DEC,\%DEL,\%GBO,\%PRO at /usr/amber7/exe/mm_pbsa.pl line 1567.
Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at /usr/amber7/exe/mm_pbsa.pl line 1645.

my input using GB model:

.....
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
@MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII ../atmtypenumbers
.....

　　　　　　　　Xiao He
　　　　　　　　hx_at_itcc.nju.edu.cn
　　　　　　　　　　2004-10-16

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