>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
Thanks!
An organic drug.Amber7 runs but refused to write the results on a file then stops.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
Use of uninitialized value in multiplication (*) at /usr/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1325.
No data for 0+0 GB GB 0
[1] Exit 26 mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
He Xiao
>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.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.itcc.nju.edu.cn
>> 2004-10-16
>>
>>
>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber.scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>= = = = = = = = = = = = = = = = = = = =
>
>
>
>
>
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>.
= = = = = = = = = = = = = = = = = = = =
致
礼！
Xiao He
hx.itcc.nju.edu.cn
2004-10-16
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Oct 16 2004 - 16:53:00 PDT
