yes, what happens, with a bit more detail, is:
- With wat.top and wat.crd: the program runs.
The output file tells me I have the correct number of atoms. But it doesn't calculate the energies because "non-bonded pairs are generated in residue base and stored as residue pairs". I'm guessing this is the waters and ions that're floating around. Even if I only select the RNA residues for the analysis this error occurs.
- With nowat.top and nowat.crd (ie, no water and no ions).
In the output file there's no number of atoms and no coordinates. On my terminal I get this error:
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
anal 0000000000476B6E Unknown Unknown Unknown
anal 0000000000475052 Unknown Unknown Unknown
anal 000000000044EC38 Unknown Unknown Unknown
anal 0000000000424036 Unknown Unknown Unknown
anal 0000000000423C97 Unknown Unknown Unknown
anal 00000000004322DA Unknown Unknown Unknown
anal 0000000000431786 Unknown Unknown Unknown
anal 0000000000409184 Unknown Unknown Unknown
anal 0000000000402ADF Unknown Unknown Unknown
anal 00000000004002D6 Unknown Unknown Unknown
anal 000000000047FA68 Unknown Unknown Unknown
anal 00000000004001EA Unknown Unknown Unknown
My input for ptraj, to strip WAT and ions, is:
trajin RNA.6.crd
strip :WAT
strip :Na+
strip :Cl-
trajout RNA.6.nowat.crd nobox
One thing I've noticed is that ptraj strips 6447 waters, but I solvated my system with 6495. Is it possible that these 48 waters flew away during the trajectory? Or doesn't ptraj recognize them?
Another thing I know is that anal needs coordinates in RESTART format, but crd is a RESTART format, isnt it? what's this "Internal Formatted Read"?
I'm sorry I have so many questions, I'm aware this program is rather old and maybe not too frequently used.
Thanks very much again,
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
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: 27 February 2013 21:08
To: AMBER Mailing List
Subject: Re: [AMBER] Error analysing an RNA trajectory with anal
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 Thu Feb 28 2013 - 03:00:02 PST
