AMBER Archive (2003)

Subject: MM-PBSA error

From: Bimo Ario Tejo (bimo7_at_linuxmail.org)
Date: Mon Feb 03 2003 - 23:56:34 CST

Dear all,

Is it possible that something wrong in Amber7 executable files? I try to run MM-PBSA and got following error messages:

Illegal character in prototype for mm_pbsa_statistics::mm_pbsa_stat : $calc_delta,$calc_dec,$input,$output,$snap_min,$snap_max at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 275.
Illegal character in prototype for mm_pbsa_statistics::output : $output,$calc_delta at /usr/local/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/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 493.
Using an array as a reference is deprecated at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 560.
Illegal character in prototype for mm_pbsa_statistics::output_decomp : $output,$calc_delta,$calc_dec at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 609.
Illegal character in prototype for mm_pbsa_statistics::calc_delta : $calc_dec at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 747.
Illegal character in prototype for mm_pbsa_statistics::map_res_pair : $j,$decind,\$mapres1,\$mapres2 at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 877.
Illegal character in prototype for mm_pbsa_statistics::map_res : $calcres,$mol at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 918.
Illegal character in prototype for mm_pbsa_statistics::map_ind_pair : $j%$decsumcom,$mol,\$maprec,\$maplig at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 946.
Illegal character in prototype for mm_pbsa_statistics::map_ind : $calcres,$com,$mol at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1028.
Illegal character in prototype for mm_pbsa_statistics::calc_ave_stdev : $calc_delta,$calc_dec at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1077.
Illegal character in prototype for mm_pbsa_statistics::read_data : \@files,$calc_dec,$snap_min,$snap_max at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1351.
Illegal character in prototype for mm_pbsa_statistics::check_completeness : $fileno,$snap,$decsum,$snap_min at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1454.
Illegal character in prototype for mm_pbsa_statistics::check_calc : \@tmp_calc at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1491.
Illegal character in prototype for mm_pbsa_statistics::reorder_files : \@files at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1515.
Illegal character in prototype for mm_pbsa_statistics::read_input : $ARGV[0],\@files at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1542.
Illegal character in prototype for mm_pbsa_statistics::calc_moments_of_distr : \@data,\$ave,\$adev,\$sdev,\$var,\$skew,\$curt at /usr/local/amber7//src/mm_pbsa/mm_pbsa_statistics.pm line 1573.
Illegal character in prototype for main::init_data : \%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 124.
Illegal character in prototype for main::read_input : $file,\%GEN,\%DEC,\%DEL,\%GBO,\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /usr/local/amber7/exe/mm_pbsa.pl line 149.
Illegal character in prototype for main::check_sanity : \%GEN,\%DEC,\%DEL,\%GBO,\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /usr/local/amber7/exe/mm_pbsa.pl line 379.
Illegal character in prototype for main::get_res_no : $str at /usr/local/amber7/exe/mm_pbsa.pl line 567.
Illegal character in prototype for main::test_par : \@,\@ at /usr/local/amber7/exe/mm_pbsa.pl line 591.
Illegal character in prototype for main::test_fil : \@,\@ at /usr/local/amber7/exe/mm_pbsa.pl line 626.
Illegal character in prototype for main::create_input : \%GEN,\%DEC,\%DEL,\%GBO,\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /usr/local/amber7/exe/mm_pbsa.pl line 650.
Illegal character in prototype for main::create_nmode_input : \%GEN,\%NMO at /usr/local/amber7/exe/mm_pbsa.pl line 685.
Illegal character in prototype for main::create_sander_input : \%GEN,\%DEC,\%DEL,\%GBO at /usr/local/amber7/exe/mm_pbsa.pl line 738.
Illegal character in prototype for main::create_delphi_input : \%DEL at /usr/local/amber7/exe/mm_pbsa.pl line 862.
Illegal character in prototype for main::create_makecrd_input : \%GEN,\%MAK,\$TRA at /usr/local/amber7/exe/mm_pbsa.pl line 925.
Illegal character in prototype for main::create_coords : \%PRO,\$TRA at /usr/local/amber7/exe/mm_pbsa.pl line 1038.
Illegal character in prototype for main::calc_energy_entropy : \%GEN,\%DEC,\%DEL,\%MOL,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 1082.
Illegal character in prototype for main::calc_NM : *OUT,$nscl,$nnmo,$ncrdfile,$npar,$sanout,$sanres,$nmodeout,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 1208.
Illegal character in prototype for main::calc_ms : $out,$pqr,$mol,$r_mol,$r_pro at /usr/local/amber7/exe/mm_pbsa.pl line 1253.
Illegal character in prototype for main::generate_pqr : $pdb,$pqr,$r_mol at /usr/local/amber7/exe/mm_pbsa.pl line 1279.
Illegal character in prototype for main::make_pqr_file : $pdb,$pqr,\%unit_rad,\%exp_rad,\@pat at /usr/local/amber7/exe/mm_pbsa.pl line 1297.
Illegal character in prototype for main::read_radii_pattern : $r_mol->{"RADII"},\%unit_rad,\%exp_rad,\@pat at /usr/local/amber7/exe/mm_pbsa.pl line 1353.
Illegal character in prototype for main::generate_pdb : $pdb,$ncrdfile,$npar,$r_pro at /usr/local/amber7/exe/mm_pbsa.pl line 1418.
Illegal character in prototype for main::calc_MM_GB_SAS : *OUT,$nsan,$sanout,$ncrdfile,$npar,$r_gen,$r_pro at /usr/local/amber7/exe/mm_pbsa.pl line 1455.
Illegal character in prototype for main::calc_PB : $OUT,$pdbbase,$outbase,\%DEL,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 1512.
Illegal character in prototype for main::calc_statistics : \%GEN,\%DEC,\%DEL,\%GBO,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 1566.
Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at /usr/local/amber7/exe/mm_pbsa.pl line 1644.

Best regards,
Bimo 

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