Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords

From: Elvis Martis <>
Date: Fri, 15 Dec 2017 14:07:14 +0000

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 <>
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

AMBER mailing list

AMBER mailing list
Received on Fri Dec 15 2017 - 06:30:05 PST
Custom Search