On Fri, Mar 21, 2014 at 8:32 PM, Nelson Max <max.cs.ucdavis.edu> wrote:
> 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?
>
Look in the tleap.out file. Do you see any error messages there?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 21 2014 - 19:00:02 PDT
