Maryam,
please note that the pmemd executable is part of the "Amber"
distribution, while almost all other executables are distributed via the
"AmberTools" collection, and there are distinct licenses for these two.
Thankfully, both sets of programs are now free for non-commercial use.
See
http://ambermd.org/GetAmber.php
But hence you may only have AmberTools installed, and now need to
license, download, and install the "Amber" set as well, where pmemd is
included. Most probably, your issues will resolve then.
(For gem.pmemd, have a look into the Amber manual, if that's really the
program you intent to run. Your input file seems to not fit the
requirements.)
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 08/03/2023 06:55 PM, Maryam Foroozmehr via AMBER wrote:
> To Whom It May Concern:
>
> It is very appreciated letting me know how to debug the below problem.
> Thank you.
>
> Simple simulation of Alanine dipeptide:
> *Part 19. Run the production MD of alanine dipeptide with pmemd:*
>
> Question: There is no "pmemd" in the bin file, instead there is
> "gem.pmemd". While running it there is the below error:
>
> ERROR: SHAKE (ntc != 1) may not be used with Amoeba or GEM!
>
> *- By considering the error, I made these changes: ntc=1,ntf=1, but then I
> got the below error:*
> *Command:* amber22_src/AmberTools/src/gem.pmemd/src/inpcrd_dat.F90 (unit =
> 9, file = '02_Heat.ncrst')
> Fortran runtime error: Bad value during floating point read
>
> Error termination. Backtrace:
> #0 0x7f3684ffd960 in ???
> #1 0x7f3684ffe4d9 in ???
> #2 0x7f368524faba in ???
> #3 0x7f36852536b9 in ???
> #4 0x7f3685254e55 in ???
> #5 0x559ec62a84f3 in __inpcrd_dat_mod_MOD_init_old_type_inpcrd_dat
> #6 0x559ec62a9d8f in __master_setup_mod_MOD_master_setup
> #7 0x559ec62d646f in MAIN__
> #8 0x559ec61e858e in main
> ^C
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Received on Sun Aug 06 2023 - 06:30:02 PDT
