AMBER Archive (2004)

Subject: Re: AMBER: error in mm_pbsa

From: Wu Yingliang (wuyliang_at_public.wh.hb.cn)
Date: Sat Oct 16 2004 - 04:52:47 CDT

Illegal characters often does not affect amber7 running, and how about your results?
By the way, your ligand is also a protein or peptide?

Yours,

Yingliang
wuyliang_at_public.wh.hb.cn

        

======= 2004-10-16 17:12:00 Orignal contents=======

>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,\,\ at /usr/amber7/exe/mm_pbsa.pl line 1513.
>Illegal character in prototype for main::calc_statistics : \,\,\,\,\ at /usr/amber7/exe/mm_pbsa.pl line 1567.
>Illegal character in prototype for main::final_clean_up : \,\ 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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