you can't use a pdb file for the reference. it must be a restart file that
matches the same atom number and order as your inpcrd.
On Thu, Apr 28, 2016 at 12:46 PM, Shukla, Saurabh <sshukla4.illinois.edu>
wrote:
> Dear Amber users,
> I am trying to do Targeted MD in amber and I am getting an error that I am
> not able to diagnose. Error is:
> "
>
> At line 288 of file set.F90
>
> Fortran runtime error: Bad value during integer read
>
> "
>
> I am attaching my amber input file for your reference. I use an
> equilibrated protein as input and give a pdb file as a reference structure.
> My atom and residue numbers in reference and simulation structure are
> matching. Although, reference structure does not contain any water
> molecules.
>
>
> I give the following command to run the simulation-
>
> sander -O -p start.top -c start.rst -i tmd.in -o start.out -r end.rst -x
> start.mdcrd -ref ref.pdb
>
>
> Please help me diagnose the problem.
>
>
> Thank You.
>
> Warm Regards,
> Saurabh Shukla,
> Second Year Graduate Student,
> Department of Chemical and Bio-molecular Engineering,
> University of Illinois at Urbana-Champaign.
>
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>
>
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Received on Thu Apr 28 2016 - 10:30:04 PDT
