HI,
Just to add to this, the perl script for mm_pbsa does not support netcdf format for the trajectory.
The python script for mmpbsa supports all formats.
Hope this helps.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 15 December 2017 19:13
To: AMBER Mailing List
Subject: Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords
On Thu, Dec 14, 2017, Investigador Química wrote:
>
> I had the Amber12 that worked well. The same calculations I tried to run on
> Amber16 newly installed on another computer. The extract_coords of Amber16
> indicates the following error
>
> At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin')
>
> Fortran runtime error: Bad value during floating point read
>
> make: *** [all] Error 141
>
> In addition the mdcrd file of the prod1 generated by Amber16 has a size of
> 3,573.oo8 unlike the same file generated by Amber12 that has a size of
> 7,231,781.
The default file format for trajectory files changed in Amber16 to netcdf.
This is probably the reason for the file size change; I don't know if
mmpbsa handles netcdf files or not, but the error message quoted above
is at a place where the code is expecting to find the older format. Set
ioutfm=0 if you want to go back to using ASCII trajectory files.
...hope this helps...dac
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Received on Fri Dec 15 2017 - 06:30:05 PST
