From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Mar 29 2007 - 07:46:19 CDT
Hi,
Please use an AMBER topology file created with Leap and not a PREP file
... PREP files are NOT topology files, they do not contain force field
information ...!!
vlad
Hidekazu WATANABE wrote:
> Hi, everyone.
> i'd like to ask a very basic question of you.
>
> I want to use an amber parameter file for NAMD simulation,
> but the program doesn't work.
> The configuration file is written as follows:
> ========
> amber yes
> ambercoor ./r800.new.pdb
> parmfile ./r800.prepin
> ========
>
> "r800.new.pdb" is a PDB format file,
> and "r800.prepin" is amber PREP file.
> Is the file of Sybyl Mol2 type, "r800.mol2" also needed?
>
> Please show me how to let NAMD program read the amber parameter files.
> These three files are attached to this E-mail.
>
>
-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533266 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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