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
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Received on Mon Feb 18 2013 - 01:30:03 PST
