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
Received on Wed Feb 27 2013 - 11:00:03 PST
