Dear Jason,
Thanks for the quick reply. I do not know if I am supposed to reply to the
AMBER mailing just or just to you, so I am doing both. I did not find any
string with "error" in the tleap.out file. In a separate e-mail just to you
I will attach the files.
On Fri, Mar 21, 2014 at 6:35 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 21:30:02 PDT
