I'm pretty sure the old perl version of mmpbsa does not support NetCDF. The
newer python version uses cpptraj under the hood so it supports any format
cpptraj does. Any reason you can't just use mmpbsa.py?
If for some reason you need the perl version you could convert the traj to
ascii format with cpptraj.
-Dan
On Fri, Jun 30, 2017 at 4:18 AM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi,
>
> Is netcdf format trajectories not compatible with mm_pbsa.pl?
>
> Because when I tried to extract snapshots for mm_pbsa (tried amber14 and
> amber16) but it gave me 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
>
> AmberTools16 Module: make_crg_hg
>
> usage: make_crd_hg < trajectory_file"
>
> But when I converted the netcdf (.nc) to ASCII trajectory (.crd), there
> was no problem at all.
>
> Can somebody please explain?
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [
> https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/icons_for_colors_32/linkedin.png
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>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Jun 30 2017 - 08:00:03 PDT
