Re: [AMBER] How to recompile AmberTools

From: Gustaf Olsson <>
Date: Thu, 25 Feb 2021 08:02:54 +0000

Hello Matthew

There are many pitfalls, depending on what you have installed and how it was installed :-)

With annoying persistence I am sticking with using the “homebrew” package manager, which has caused me some grief in the past.

You should, if you have not installed other compilers or use any strange system settings, be able to follow the recommendations on the website.

You need to install a fortran compiler, recommended is gfortran though version 9 or previous.

Then it should be as simple as running './run_cmake' in the "amber20_src/build/“ directory and if successfully executed, 'make install’

If compilation fails reporting something mentioning “yylex”, then add these lines:

    int yyerror( char *sStr );
    int yylex();


   extern int yyparse();

which is found around line 199 in the "amber20_src/AmberTools/src/leap/src/leap/parser.y” directory.

Good luck and best regards
// Gustaf

> On 24 Feb 2021, at 21:04, Matthew Guberman-Pfeffer <> wrote:
> Hi Gustaf,
> I’m using Mac OS X 10.15.7 (Catalina). Are there specific instructions or pitfalls that I should look out for given this OS?
> Best,
> Matthew
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Received on Thu Feb 25 2021 - 00:30:02 PST
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