On Fri, Jun 29, 2018, Portillo, Jennifer wrote:
>
> 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
>
> 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'm a little lost here: it looks like you pointed sander to the
"protein.prtmop file", not the "strip.protein.prmtop" file that the
cpptraj script created. Is that what you intended?
Look at the FORCE_FIELD_TYPE section in both the original prmtop file
(that you used for the MD simulation) and any that cpptraj may have
created. Are they the same? Can you post what is in that section of
the protein.prmtop file?
As an aside, cpptraj can now compute energies itself: you don't need to
go through a separate sander step: see the "energy" or "esander"
actions.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 29 2018 - 18:30:03 PDT
