Re: It doesn't work with using amber files.

From: campen_at_geosc.psu.edu
Date: Thu Mar 29 2007 - 11:28:36 CDT

Hidekazu:

If you specify ambercoor I think you want to use a .coor file (could be
wrong about the suffix). You can use your pdb with an Amber topology but
in that case you just want the usual command,

coordinates XXX.pdb

Kramer

> 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.
>>
>>
>
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