Not sure if this could be the problem but try changing your pdb for reference structure into a .inpcrd file.
Charlie
________________________________________
From: Shukla, Saurabh [sshukla4.illinois.edu]
Sent: Thursday, April 28, 2016 9:46 AM
To: amber.ambermd.org
Subject: [AMBER] Targeted MD error
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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 28 2016 - 10:00:04 PDT
