It doesn't work with using amber files.

From: Hidekazu WATANABE (evergreen_tow_at_yahoo.co.jp)
Date: Thu Mar 29 2007 - 07:09:25 CDT

• Next message: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Previous message: Peter Freddolino: "Re: Pressure Discrepancy"
• Next in thread: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Reply: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Reply: Hidekazu WATANABE: "Re: It doesn't work with using amber files."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

--------------------------------------
[10th Anniversary] Check Out the Special Final Sale
http://pr.mail.yahoo.co.jp/10thann/

• application/octet-stream attachment: r800.new.pdb

• Next message: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Previous message: Peter Freddolino: "Re: Pressure Discrepancy"
• Next in thread: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Reply: Vlad Cojocaru: "Re: It doesn't work with using amber files."
• Reply: Hidekazu WATANABE: "Re: It doesn't work with using amber files."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:31 CST