AMBER Archive (2003)

Subject: AMBER: Re: Nmode problem

From: Wu Yingliang (wuyliang_at_public.wh.hb.cn)
Date: Sat Nov 29 2003 - 21:52:15 CST

Dear Dr. Holger Gohlke,

I highly appreciate your reply!

All other examples from mm_pbsa examples except "Nmode" have no problem to run. The usful messages during running, I think, are as following:

file1: nmode_lig.1.out

          *******************************************************
          Initiate the NMODE module of AMBER 7
          *******************************************************

  File generated by mm_pbsa.pl
       ntrun maxcyc ibelly drms
          1 100 0 0.10E+01
       rcut scnb scee dielc idiel
     99.00000 2.00000 1.20000 4.00000 0
      nsave dfpred bdwnhl smx emx alpha ndiag
         20 0.01000 0.10000 0.08000 0.30000 0.80000 10
 ipol = 0
 i3bod = 0
 nvect = 0
     Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 01/07/02 Time = 15:05:50

    PARM file has the title:
                                                                                     
   Memory allocation :

           1 1242 2483 2525 2567
        2659 2751 2843 2935 3027
        3060 3093 3126 3155 3260
        3365 3365 3365 3365 8329
           0 1 1242 2484 3726
        3923 3999 4077 4711 5345
        5979 6597 7215 7833 9271
       10709 12147 13585 14416 15247
       16078 16909 21312 25715 30118
       34521 38924 43327 47730 52133
       56536 60939 67783 69024 72749
       75233 76475 13293 17016 24462
       77717 0 78959 0 0
           0 0 0 0 70265
       71507 12052 0

     Duplicated 0 dihedrals

     Duplicated 0 dihedrals
   Memory allocation :

           1 1242 2483 2525 2567
        2659 2751 2843 2935 3027
        3060 3093 3126 3155 3260
        3365 3365 3365 3365 8329
           0 1 1242 2484 3726
        3923 3999 4077 4711 5345
        5979 6597 7215 7833 9271
       10709 12147 13585 14416 15247
       16078 16909 21312 25715 30118
       34521 38924 43327 47730 52133
       56536 60939 67783 69024 72749
       75233 76475 13293 17016 24462
       78959 6957930 80201 6957931 6991438
     6995161 0 0 0 70265
       71507 12052 0

Total memory required : 20855890 real words

Total memory avail : 3500000 real words

Total memory required : 80201 integer words

Total memory avail : 4000000 integer words

Maximum nonbond pairs 3919798
increase the real memory by 17355890 words

file2: mm_pbsa.log

=>> Init data
    Presuming executables of amber suite to be in /home/whu/amber7/exe

=>> Reading input parameters
    Found PREFIX => ras_raf_II_wt
    Found PATH => ../01_GenerateSnapshots/
    Found COMPLEX => 0
    Found RECEPTOR => 0
    Found LIGAND => 1
    Found LIGPT => ../raf_wt.prmtop
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 0
    Found GB => 0
    Found PB => 0
    Found MS => 0
    Found NM => 1
    Found DIELC => 4
    Found MAXCYC => 500
    Found DRMS => 0.1
    Found DELPHI => /home/whu/Delphi/LINUX/delphi

=>> Checking sanity
    Checking GENERAL
    Checking NM

=>> Creating input
    Nmode input

=>> Calculating energy / entropy contributions
    Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1
        Minimize structure
        Calc entropy

message during mm_pbsa running:

[whu_at_localhost 04_MMPBSA_Nmode]$ mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
Illegal character in prototype for mm_pbsa_statistics::mm_pbsa_stat : $calc_delt
a,$calc_dec,$input,$output,$snap_min,$snap_max at /home/whu/amber7/src/mm_pbsa/m
m_pbsa_statistics.pm line 275.
Illegal character in prototype for mm_pbsa_statistics::output : $output,$calc_de
lta at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 363.
Illegal character in prototype for mm_pbsa_statistics::output_snap : $output,$ca
lc_delta,$snap_min at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 49
3.
Using an array as a reference is deprecated at /home/whu/amber7/src/mm_pbsa/mm_p
bsa_statistics.pm line 560.
Illegal character in prototype for mm_pbsa_statistics::output_decomp : $output,$
calc_delta,$calc_dec at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line
609.
Illegal character in prototype for mm_pbsa_statistics::calc_delta : $calc_dec at
 /home/whu/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 /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line
877.
Illegal character in prototype for mm_pbsa_statistics::map_res : $calcres,$mol a
t /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 918.
Illegal character in prototype for mm_pbsa_statistics::map_ind_pair : $j%$decsum
com,$mol,\$maprec,\$maplig at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm
 line 946.
Illegal character in prototype for mm_pbsa_statistics::map_ind : $calcres,$com,$
mol at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1028.
Illegal character in prototype for mm_pbsa_statistics::calc_ave_stdev : $calc_de
lta,$calc_dec at /home/whu/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 /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm l
ine 1351.
Illegal character in prototype for mm_pbsa_statistics::check_completeness : $fil
eno,$snap,$decsum,$snap_min at /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.p
m line 1454.
Illegal character in prototype for mm_pbsa_statistics::check_calc : \@tmp_calc a
t /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1491.
Illegal character in prototype for mm_pbsa_statistics::reorder_files : \@files a
t /home/whu/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1515.
Illegal character in prototype for mm_pbsa_statistics::read_input : $ARGV[0],\@f
iles at /home/whu/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 /home/whu/amber7/src/mm_pbsa/mm
_pbsa_statistics.pm line 1573.
Illegal character in prototype for main::init_data : \%PRO at /home/whu/amber7/e
xe/mm_pbsa.pl line 124.
Illegal character in prototype for main::read_input : $file,\%GEN,\%DEC,\%DEL,\%
GBO,\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /home/whu/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 /home/whu/amber7/exe/mm_pbsa.pl line 379.
Illegal character in prototype for main::get_res_no : $str at /home/whu/amber7/e
xe/mm_pbsa.pl line 567.
Illegal character in prototype for main::test_par : \@,\@ at /home/whu/amber7/ex
e/mm_pbsa.pl line 591.
Illegal character in prototype for main::test_fil : \@,\@ at /home/whu/amber7/ex
e/mm_pbsa.pl line 626.
Illegal character in prototype for main::create_input : \%GEN,\%DEC,\%DEL,\%GBO,
\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /home/whu/amber7/exe/mm_pbsa.pl line 650.
Illegal character in prototype for main::create_nmode_input : \%GEN,\%NMO at /ho
me/whu/amber7/exe/mm_pbsa.pl line 685.
Illegal character in prototype for main::create_sander_input : \%GEN,\%DEC,\%DEL
,\%GBO at /home/whu/amber7/exe/mm_pbsa.pl line 738.
Illegal character in prototype for main::create_delphi_input : \%DEL at /home/wh
u/amber7/exe/mm_pbsa.pl line 862.
Illegal character in prototype for main::create_makecrd_input : \%GEN,\%MAK,\$TR
A at /home/whu/amber7/exe/mm_pbsa.pl line 925.
Illegal character in prototype for main::create_coords : \%PRO,\$TRA at /home/wh
u/amber7/exe/mm_pbsa.pl line 1038.
Illegal character in prototype for main::calc_energy_entropy : \%GEN,\%DEC,\%DEL
,\%MOL,\%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1082.
Illegal character in prototype for main::calc_NM : *OUT,$nscl,$nnmo,$ncrdfile,$n
par,$sanout,$sanres,$nmodeout,\%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1208Illegal character in prototype for main::calc_ms : $out,$pqr,$mol,$r_mol,$r_pro
at /home/whu/amber7/exe/mm_pbsa.pl line 1253.
Illegal character in prototype for main::generate_pqr : $pdb,$pqr,$r_mol at /hom
e/whu/amber7/exe/mm_pbsa.pl line 1279.
Illegal character in prototype for main::make_pqr_file : $pdb,$pqr,\%unit_rad,\%
exp_rad,\@pat at /home/whu/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 /home/whu/amber7/exe/mm_pbsa.pl line 1353.
Illegal character in prototype for main::generate_pdb : $pdb,$ncrdfile,$npar,$r_
pro at /home/whu/amber7/exe/mm_pbsa.pl line 1418.
Illegal character in prototype for main::calc_MM_GB_SAS : *OUT,$nsan,$sanout,$nc
rdfile,$npar,$r_gen,$r_pro at /home/whu/amber7/exe/mm_pbsa.pl line 1455.
Illegal character in prototype for main::calc_PB : $OUT,$pdbbase,$outbase,\%DEL,
\%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1512.
Illegal character in prototype for main::calc_statistics : \%GEN,\%DEC,\%DEL,\%G
BO,\%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1566.
Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at /home/w
hu/amber7/exe/mm_pbsa.pl line 1644.
        /home/whu/amber7/exe/nmode -O -i nmode_lig.in -o nmode_lig.1.out -c sanm
in_lig.1.restrt -p ../raf_wt.prmtop not running properly
[whu_at_localhost 04_MMPBSA_Nmode]$

It seems that memory is not enough for calcuation, right? As for my computer, the meory is 512M, and swap memory is 1G.

Best regards,

Wu Yingliang

2003-11-30
==================================
College of Life Sciences
Wuhan University
Wuhan 430072
China
Email: wuyliang_at_public.wh.hb.cn
==================================

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