On 2012-01-11, at 1:07 AM, Sudarshan Debnath wrote:
> Dear Sir,
>
> When I use (./rism1d) command in terminal then it shows ‘input file not specified’, but when I used (./rism3d or ./rism3d.snglpnt or sander.RISM as given in the Amber11 users’ manual at page 62) all of it shows ‘no such file or directory’. In exe folder 75 executable files are present (such as sander, tleap, rism1d, nab etc), but there is no executable file having name (rism3d or sander.RISM or rism3d.snglpnt). So it seems that rism3d.snglpnt is not build during Amber tools installation.
>
> You and Dan suggested that to built rism3d.snglpnt recompilation of Amber Tools is necessary. Is the recompilation same process like Amber tools installation given in Amber tools users’ manual from page 13 to 14? Before recompiling the Amber tools I need your suggestion. As in my existing system already Amber tools are compiled, so during recompilation is it necessary to delete or remove the previous file? If no, then I want to do the following step-
>
>
>
> Create a directory under usr/local (say usr/local/software).
>
>
>
> (By the way, previously Amber tools was installed in usr/local directory.)
>
>
>
> Keep two zip files in software folder (Amber11.tar.bz2 and AmberTools-1.4.tar.bz2).
>
>
rism3d.snglpnt is only in AmberTools 1.5. sander.RISM has not been released because of license issues.
You do not need Amber11 for rism3d.snglpnt and if this is your primary interest, it may be easier to just install AmberTools 1.5 by itself. If not, there are instructions on the website for building Amber11 with AmberTools 1.5.
As for the steps you used to build Amber and AmberTools they looked fine (though you appear to have done the same thing twice) except you need to apply the bugfix patches. These are also found on the website. There are two that are specifically for RISM so it is important to apply these.
Hope this helps,
Tyler
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
848-445-5239
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Received on Tue Jan 10 2012 - 23:00:02 PST
