AMBER Archive (2008)

Subject: Re: AMBER: a link for Amber ff ported to Charmm

From: Alan (alanwilter_at_gmail.com)
Date: Sun Jul 20 2008 - 00:50:22 CDT

Thank guys! I am aware of this (as mentioned as well in Klauda's link)
and I intend to use NAMD which has a "flag" to enable amber instead of
default charmm.

Cheers,
Alan

On Sat, Jul 19, 2008 at 11:28 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> You also need to turn on AMBER's electrostatic scaling in place of CHARMM's.
>
> See fcm/consta.fcm
>
> ##IF AMBER
> C Note: This value provides compatibility with electrostatics in AMBER
> PARAMETER (CCELEC=332.0522173D0)
>
> Good luck,
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Adrian Roitberg
>> Sent: Saturday, July 19, 2008 3:11 PM
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: a link for Amber ff ported to Charmm
>>
>> Alan,
>> One associated comment,
>>
>> Even if you could implement the amber-style force fields into charmm,
>> remember please that charmm's default for the scaling of the 1-4
>> non-bonded interactions is different than amber's !
>>
>> Unless this is is taken care somewhere in charmm or its input, you will
>> get different answers than 'canonical' amber.
>>
>> a.
>>
>>
>> Alan wrote:
>> > Thanks a lot Dave.
>> >
>> > I am not kidding, I was doing exactly this prior your mention but link
>> > to Kluada's was saying 'access not allowed' and could only see it in
>> > Google cache.
>> >
>> > Fortunately it's back apparently. Many thanks again.
>> >
>> > Alan
>> >
>> > On Sat, Jul 19, 2008 at 7:29 PM, David A. Case <case_at_scripps.edu> wrote:
>> >> On Sat, Jul 19, 2008, Alan wrote:
>> >>> I tried some googling without much success. Can someone point me links
>> >>> referencing amber ff (94, 99 etc.) written in charmm format for charmm
>> >>> of course.
>> >>>
>> >>> I know that with amberTools comes cornell (amber94) for charmm, but a
>> >>> link and other possible ff ported would be really interesting for me.
>> >> Go here: http://www.glue.umd.edu/~jbklauda/research/download.html
>> >>
>> >> (I got this from http://ambermd.org, by following the "using the Amber
>> force
>> >> field in CHARMM" link).
>> >>
>> >> ...dac
>> >>
>> >> -----------------------------------------------------------------------
>> >> The AMBER Mail Reflector
>> >> To post, send mail to amber_at_scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> >> to majordomo_at_scripps.edu
>> >>
>> >
>> >
>> >
>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>>
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu