On Fri, Sep 18, 2020, Renato Araujo wrote:
>
>friends, i'm trying to minimize a protein binding system, but i get the
>following message on the terminal.
>
>Program received signal SIGSEGV: Segmentation fault - invalid memory
First: try your calculation in serial rather than parallel mode...that
might tell you something.
Second: look at the output, when does the error happen? (Before the
first step, sometime later? Are there any clues about what might be
wrong? Does it look like it read the cntrl namelist correctly? (You
have bad syntax there, but maybe your compiler will accept it.
>Mnimization HIDROG + WAT
>& cntrl
^^^^^^^ leave out the space between '&' and 'cntrl'
>imin = 1, ntx = 1,
>ntpr = 1, ntwr = 5000, ibelly = 1,
>maxcyc = 5000, ncyc = 2000, drms = 0.001
>& end
^^^^^ leave out the space between '&' and 'end'; better replace this
whole line with '/', which is the correct way to end a namelist block
Much of the material below seems very odd. Try leaving out ibelly, just
to see if that is the problem. Again look at the output: it will tell
you if the program (a) even read these lines; (b) choked on lines like
'THERE IS' and 'AND'. (Set maxcyc=10 for test runs, until you can get
things to work.)
>Residues moving during minimization
>FIND
>* H * *
>* HC * *
>* H1 * *
>* H2 * *
>* H3 * *
>* THERE IS * *
>* H4 * *
>* H5 * *
>* HO * *
>* HS * *
>* HP * *
>* HZ * *
>SEARCH
>RES 1 306
>END
>AND
>RES 311 18902
>END
>END
>
...dac
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Received on Fri Sep 18 2020 - 19:00:02 PDT
