Hi,
This is a wild shot in the dark since I have never used the program,
but when you use the topology/coordinate files without water, have you
stripped the box coordinates from the trajectory? E.g. using the
ptraj/cpptraj input:
trajout nowat.crd nobox
-Dan
On Wed, Feb 27, 2013 at 11:44 AM, Amparo Garcia Lopez
<Amparo.GarciaLopez.unige.ch> wrote:
> Dear all,
>
> After generating a MD trajectory of a solvated RNA molecule with amber11, I was trying to obtain the base stacking energies using the old program "anal" (amber9). I have both one question and one problem regarding this:
>
> - This is pure ignorance from my side, but was anal left behind simply because ptraj took over? can I do this same stacking energy analysis with ptraj?
>
> - Second, and this is my technical problem, this is my input for "anal":
>
> test of anal energies, RNA_200ns
> 1 0 0 0 0 1
> 0 0.0 0.0 0.0 0.0
> 1 0 0 0 0 0
> 99.0 2.0 1.2 1.0
> 1 10.0 10.0 10.0 10.0 10.0 10.0 20.0 10.0 10.0
> ENERGY
> RES 1 21
> END
> END
> STOP
>
> e.g. of command line:
> anal -i analin -o analout -p RNA.vac.top -c RNA.6.vac.crd
>
> I've tried using topology and coordinate files both with and without water.
> What I get is this error:
>
> Image PC Routine Line Source
> anal 0000000000476B6E Unknown Unknown Unknown
> anal 0000000000475052 Unknown Unknown Unknown
> anal 000000000044EC38 Unknown Unknown Unknown
> etc etc
>
> Inside the analout file I see that there are no atomic coordinates.
>
> What have I done wrong? I know the problem is in my files, as I have run the "control files" from the amber/test/vac_rna folder w/o problem. But I just don't know what to change. I have processed these same files with ptraj before, to do clustering, avg.pdb, combining trajectories, etc etc, so they can't be that terrible??
>
> This is my first time using "anal". Any ideas?
>
> Thanks very much in advance.
>
> Amparo Garcia-Lopez, Ph.D.
>
> Pharmaceutical Biochemistry
> School of Pharmaceutical Sciences
> University of Geneva
> Quai Ernest-Ansermet 30
> 1211 Genève 4 - Switzerland
>
> Tel: +41 (0)22 379 3376
> Fax: +41 (0)22 379 3360
>
> e-mail: Amparo.GarciaLopez.unige.ch
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Feb 27 2013 - 12:30:02 PST
