Hi,
I ran MD on a protein in its solvent environment and want to calculate the
energy of the protein alone during the trajectory.
I used cpptraj to create a topology (prmtop) file of the protein alone and
the trajectory file for protein alone.
When I visualize the protein only trajectory with protein only prmtop file
using VMD, I am able to visualize the protein trajectory. However, when I
use these files in sander to get the energies using imin=5, I get the
following error:
At line 244 of file rdparm.F90 (unit = 8, file = 'protein.prmtop')
Fortran runtime error: Bad value during integer read
We are using AmberTools17. The line 244 of
$AMBERHOME/AmberTools/src/sander/rdparm.F90
is reading iscratch and ffdesc.
The script that is used for cpptraj is:
parm protein.prmtop
trajin file.nc <
http://d2_gs_gtp_step6.nc/>
trajin file.nc <
http://d2_gs_gtp_step7.nc/>
strip !: 1-100 outprefix strip
trajout file.nc <
http://d2_gs_gtp_step6_7.nc/>
go
exit
I have tried making a few changes, but I keep getting the same error. Any
help will be appreciated.
Thank you,
Jennifer
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Received on Fri Jun 29 2018 - 07:30:03 PDT
