AMBER Archive (2004)

Subject: Re: AMBER: error in mm_pbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sat Oct 16 2004 - 08:53:36 CDT

Xiao He schrieb:
>
> 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
> .....

The illegal characters are due to an earlier version of perl (under
which the mm_pbsa scripts have been developed for amber7) that allowed
to have variable names etc. in function prototypes. These are just
warnings that don't affect the results.

Best regards

Holger
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