Hi,
you need to increase the parameter MAXMEMX in sizes.h in
$AMBERHOME/src/nmode (at least) to the value given below:
> Total memory required : 20855890 real words
Then recompile and reinstall nmode. This should alleviate the problems
with nmode.
With respect to the "Illegal character in prototype ..." messages: this
is due to new rules as to define function prototypes in perl versions
higher than 5. The only workaround I know here is to run mm_pbsa with a
perl version that starts with "5....".
Best regards
Holger
> 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.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,$outbase,\%DEL,
> \%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1512.
> Illegal character in prototype for main::calc_statistics : \%GEN,\%DEC,\%DEL,\%G
> BO,\%PRO at /home/whu/amber7/exe/mm_pbsa.pl line 1566.
> Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at /home/w
> hu/amber7/exe/mm_pbsa.pl line 1644.
> /home/whu/amber7/exe/nmode -O -i nmode_lig.in -o nmode_lig.1.out -c sanm
> in_lig.1.restrt -p ../raf_wt.prmtop not running properly
> [whu.localhost 04_MMPBSA_Nmode]$
>
> 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.public.wh.hb.cn
> ==================================
--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie
Marie-Curie-Str. 9
60439 Frankfurt/Main
Germany
Tel.: (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke.bioinformatik.uni-frankfurt.de
URL: http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Wed Jan 14 2004 - 15:53:02 PST
