From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Apr 27 2007 - 10:19:56 CDT
please check the amber website and/or AMBER user manual for that information
http://amber.scripps.edu/
vlad
> Huy N. Ha wrote:
>
>> Well, what i'm particularly after is an example of the content that
>> would be in that GVX.top file (the parameter/topology file, parmtop
>> format used by AMBER) not the setup of the NAMD configuration file to
>> use with an AMBER force field, which is what i think you're referring
>> to. Hope that clarifies it?
>>
>> Mr. Huy Ha
>> B. Med. Chem. Honours Student
>> Dept. of Medicinal Chemistry
>> Victorian College of Pharmacy
>> Monash University
>> 381 Royal Parade
>> Parkville 3052
>> Phone No: 99039136
>>
>>
>>
>> -----Original Message-----
>> From: wang [mailto:c00jsw00_at_nchc.org.tw]
>> Sent: Fri 4/27/2007 5:43 PM
>> To: Huy N. Ha; namd-l_at_ks.uiuc.edu
>> Subject: Re: namd-l: Amber PARM Input File Example?
>>
>> Huy N. Ha ??:
>>
>> > I was wondering if anyone has an example of a PARM format file,
>> > generated via AMBER 6+ (preferably 7 and above).
>> > I am planning to use the AMBER force field, and generate custom PARM
>> > files to use with NAMD. TIA
>> >
>> > Mr. Huy Ha
>> > B. Med. Chem. Honours Student
>> > Dept. of Medicinal Chemistry
>> > Victorian College of Pharmacy
>> > Monash University
>> > 381 Royal Parade
>> > Parkville 3052
>> > Phone No: 99039136
>> >
>> Hi ,
>> Followed the example :
>>
>> ______________________________________________________________
>> # Input
>> amber on # Specify this is AMBER force field
>> parmfile GVX.top # Input PARM file
>> ambercoor GVX.crd # Input coordinate file
>> _______________________________________________________________
>>
>> good luck
>>
>> Y.T Wang
>
>
-- ---------------------------------------------------------------------------- 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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