Re: [AMBER] flag dihedrals in the .prmtop

From: Z.Xiao <zfengxiao.126.com>
Date: Wed, 29 Dec 2010 17:38:23 +0800 (CST)

Thank you very much! By the way,In the specification it said that If the third atom is negative, this implies that the end group interations are to be ignored. Could you interpret what is the end group interations ? Does it mean that the interaction of the first and the fourth atoms descriped by dihedral which type is single cosine function and the nonbond interaction are irrelated when the foecefield is designed?



At 2010-12-29 16:24:04úČ"Jason Swails" <jason.swails.gmail.com> wrote:

>On Wed, Dec 29, 2010 at 12:43 AM, Z.Xiao <zfengxiao.126.com> wrote:
>
>> Hi all,I'm a fresher for amber. I am puzzling over the flag dihedrals in
>> the .prmtop file.
>> for example,the dihedral 3 6 9 12 had two definitions,3 6 9 12 4 and 3 6 -9
>> 12 5 in my .prmtop
>> file.Here 4 and 5 represents different dihedral types obviously.Which is
>> appropriate? or was
>> the dihedral descriped by the sum of the two cosine functions above?
>>
>
>This indicates that it is a multi-term dihedral (or part of a ring system).
>See http://ambermd.org/formats.html for a description of the prmtop file
>which was recently updated.
>
>Good luck!
>Jason
>
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>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Graduate Student
>352-392-4032
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Received on Wed Dec 29 2010 - 02:00:04 PST
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