I am a new user of AmberTools, whose force laws I eventually hope to modify
so that it can preserve the hydrogen bonding that I created with an inverse
kinematics tool called ProteinShop that is oblivious to other forces like
atom collisions, without having the beta sheets I have constructed
destroyed by the initial attempt to relieve the bad collisions.
In my first attempt to try out AmberTools, I compiled the following program
mytest.nab
molecule m;
printf("%s %s\n", argv[1], argv[2]);
m = getpdb_prm(argv[2],
"/home/max/Amber/amber12/dat/leap/cmd/leaprc.ff99SB", "", 0);
putpdb("temp.pdb", m);
using the command
nab mytest.nab -o mytest
I then ran
mytest T0612_barrel.pdb
which properly echoes my input and then gave the error in the subject line
of this message:
[max.tree mytest]$ mytest T0612_barrel.pdb
mytest T0612_barrel.pdb
Running: /home/max/Amber/amber12/bin/teLeap -s -f
leap.in-I/home/max/Amber/amber12/dat/leap/cmd
-I/home/max/Amber/amber12/dat/leap/parm
-I/home/max/Amber/amber12/dat/leap/prep
-I/home/max/Amber/amber12/dat/leap/lib > tleap.out
Reading parm file (tprmtop)
Error: EOF when searching for tprmtop
The above commands did result in the creation of a file called tprmtop in
the directory from which I was running the program, but that file is empty.
Can anyone tell me what is going wrong?
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Received on Fri Mar 21 2014 - 18:00:03 PDT
