The remarks in your output file suggest this is an XPLOR PSF file, is that
correct?
What happens if you use -xpsf instead of -psf to specify your PSF file?
Good luck,
Jason
On Mon, Feb 18, 2013 at 4:04 AM, Massimiliano Porrini <
m.porrini.iecb.u-bordeaux.fr> wrote:
> Dear Amber users,
>
> One week ago I had posted the following email, but I have not
> received any feedback about it yet.
>
> If any of you has any tip on what might be the problem in generating
> topology and coordinates files with Chamber would be really appreciated.
>
> Thanks and have a nice day,
>
>
> ---------- Forwarded message ----------
> From: Massimiliano Porrini <m.porrini.iecb.u-bordeaux.fr>
> Date: 11 February 2013 19:05
> Subject: PSF file, atom radii and chamber
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Dear all,
>
> I have trajectories in dcd format with PSF topology files and I would need
> to use cpptraj of AT12 to calculate the SASA, either with surf or molsurf
> program.
>
> Both surf and molsurf require the atom radii parameters in the
> topology/parameter file,
> and PSF files do not contain them.
>
> I have been trying to convert PDB and PSF files into crd and prm files
> using
> chamber, so as to include the atom radii, but the program stops producing
> the error shown in the attachment.
>
> Any hint/help on how to work around this will be really appreciated.
> Thanks a lot in advance.
>
> ATB,
>
> --
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> FRANCE
>
> Tel : 33 (0)5 40 00 30 31
> Fax : 33 (0)5 40 00 22 00
> http://www.iecb.u-bordeaux.fr/
> Emails: m.porrini.iecb.u-bordeaux.fr
> M.Porrini.ed.ac.uk
> maxp.iesl.forth.gr
> mozz76.gmail.com
>
>
> --
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> FRANCE
>
> Tel : 33 (0)5 40 00 30 31
> Fax : 33 (0)5 40 00 22 00
> http://www.iecb.u-bordeaux.fr/
> Emails: m.porrini.iecb.u-bordeaux.fr
> M.Porrini.ed.ac.uk
> maxp.iesl.forth.gr
> mozz76.gmail.com
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 18 2013 - 05:30:02 PST
