[AMBER] cpptraj and sander

From: Portillo, Jennifer <jennifer.portillo.387.my.csun.edu>
Date: Fri, 29 Jun 2018 07:15:05 -0700


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

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/>



I have tried making a few changes, but I keep getting the same error. Any
help will be appreciated.

Thank you,

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Received on Fri Jun 29 2018 - 07:30:03 PDT
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