Ahh, yesss you're correct about the 48 ions :-)
Thanks very much for your help. Still not sure that the problem is in the anal.in as the same script works for the control tests. Anal also runs for the trajectory with waters if I specify a small cutoff (so that there are not millions of non-bound residues). But I don't want waters in my analysis, so I'll try to use cpptraj as you suggest and VMD to double check.
Thanks 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: Jason Swails [jason.swails.gmail.com]
Sent: 28 February 2013 14:23
To: AMBER Mailing List
Subject: Re: [AMBER] Error analysing an RNA trajectory with anal
On Thu, Feb 28, 2013 at 5:42 AM, Amparo Garcia Lopez <
Amparo.GarciaLopez.unige.ch> wrote:
> 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-
>
You can do these with one command:
strip :WAT,Na+,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?
>
Do you have 48 ions? tleap replaces water molecules with ions as long as
you add the solvent first (which is the recommended practice). You can use
cpptraj or ParmEd from AmberTools 12 to generate a stripped topology and
visualize your trajectory. That's the best way to determine if your
trajectory and topology files are compatible (VMD is a good option here).
> 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"?
>
This is a Fortran-specific error message. Since I've never even seen the
anal source code, all I can say is what this error message means. A common
way of casting from a string to either an integer or a floating point
number in Fortran is to use the "read" intrinsic---only the "unit" is a
character array. So something like this:
read(my_string, '(i10)') i
This will convert the contents of my_string into an integer and store its
value in i. If the contents of my_string is not an integer (with or
without whitespace), then you'll get an "internal formatted read" (with the
intel compilers). Normally, you'd get the file unit number, but there is
no unit number when read is used on a string. This is most common when
used with a form of free-format parsing done in Fortran (with unprotected
reads) -- so the error is likely in one of the parts of the input file with
free-format input.
I'm sorry I have so many questions, I'm aware this program is rather old
> and maybe not too frequently used.
>
It's not even distributed anymore ;). At this point I've reached beyond
the extent of my experience with anal.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 28 2013 - 08:00:03 PST
