AMBER Archive (2004)

Subject: Re: AMBER: Errors in MM-PBSA???

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 21 2004 - 06:37:39 CST

ML schrieb:
>
> Dear AMBER community,
> as I'm running mm_pbsa calculations I get the following messages
> irrespective of whether the calculation completes or fails. Is it some
> serious problem or bad compilation? Does it affect the results?

>From an older answer to a related question:

>>>>>
 the reason for the messages below is that earlier versions of perl
 (under which the mm_pbsa scripts were developed) than v.5.8.0 allowed
to
 have alphanumeric characters in function prototypes, while the latest
 one does not anymore (i.e. "sub foo(@array)" was allowed, while now it
 must be "sub foo(@)"). The documentation of 5.8.0 says that at the
 moment "just" an optional warning is generated, which may become a
fatal
 error in future releases.
<<<<<

As far as I know, it shouldn't affect the results.

Best regards

Holger

>
> Thanks for your replies.
>
> Regards,
>
> Martin Lepsik
> --------
> Illegal character in prototype for mm_pbsa_statistics::calc_stat :
> \%GEN,\%DEC,\%DEL,\%GBO,\%PRO at
> /usr/local/programs/amber7-large/src/mm_pbsa/mm_pbsa_statistics.pm line 274.
>
> --
> Using an array as a reference is deprecated at /usr/local/programs/amber7-large/src/mm_pbsa/mm_pbsa_statistics.pm line 648.
> -----
> Illegal character in prototype for mm_pbsa_statistics::mm_pbsa_stat : $calc_delta,$calc_dec,$input,$output,$snap_min,$snap_max at /usr/local/programs/amber7-large/src/mm_pbsa/mm_pbsa_statistics.pm line 352.
>
> Illegal character in prototype for main::check_sanity : \%GEN,\%DEC,\%DEL,\%GBO,\%MOL,\%NMO,\%MAK,\%PRO,\$TRA at /usr/local/programs/amber7-large/exe/mm_pbsa.pl line 379.
>
> -----------
> Martin Lepsik
> Dept. of Molecular Modeling
> Institute of Organic Chemistry & Biochemistry
> Czech Academy of Sciences
> phone: +420-220 183 540
> fax:+420-220 183 292
> e-mail:lepsik_at_uochb.cas.cz
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

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_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

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