[gmx-users] Topology dihedral or improper dihedral

[Justin A. Lemkul]

XUEMING TANG wrote:
> Thank you for your reply, Lina. I did try the prodrg server before. For 
> A molecule, there is no improper dihedral. A just has one dihedral for 
> the head group. For B molecule, it gives improper dihedral of the tetra 
> nitrogen. I am wondering what is the criteria or at least a guidance of 
> what could be the best choice for the topology file. Or any choices 
> could be right and I have to try which one provide consistent results 
> with experiment by trial?  
> 

I see no reason why a quaternary nitrogen would need an improper dihedral 
assigned to it.  Some impropers in Gromos96 are applied to tetrahedral groups 
like alpha-carbons because there is no explicit H atom present, thus the 
stereochemistry is maintained with an improper so that the groups do not invert. 
  With four explicit substituents, an improper should not be necessary.

-Justin

> Best!
> Xueming
> 
> On Sun, Nov 13, 2011 at 9:57 AM, lina <lina.lastname at gmail.com 
> <mailto:lina.lastname at gmail.com>> wrote:
> 
>     On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <yujan2007 at gmail.com
>     <mailto:yujan2007 at gmail.com>> wrote:
>      > Hi there
>      >
>      > I am trying to build up a topology file for a tetra nitrogen
>     molecule using
>      > Gromos UA and OPLS UA force field. Following are the molecules.
>      >
>      > 1. for                      C
>      >                               |
>      >  A.  C-C-C-C-C-C-C-N-C         and
>      >                               |
>      >                              C
>      >
>      >                               C
>      >                                |
>      >  B.   C-C-C-C-C-C-C-N-C-C-C-C-COOH
>      >                                |
>      >                               C
>      >
>      > I have several questions:
>      >
>      > For A, the first molecule, should I use improper dihedral for the
>     N-(CH3)3
>      > or proper dihedral for C-C-N-C with multi 3 for the head group?
>     Is there any
>      > differences when using different force field (GROMOS and OPLS-UA)?
>      > For B, the second molecule, should I use improper dihedral for
>     the N-(CH3)3
>      > or proer dihedral for C-C-N-C with multi 2? Is there any
>     differences when
>      > using different force field (GROMOS UA and OPLS UA)?
>      >
>      > The first expression about improper didedral is a planer
>     restriction. When
>      > read the manual it also refers to the tetrahedral structure like
>     this tetra
>      > nitrogen functional group. My question is when it has
>      > really long hydrocarbon tail, I guess it will be hard to flip over to
>      > the mirror images. Or it is not true in the simulation?
> 
>     You may take one built by other server, such as
>     http://davapc1.bioch.dundee.ac.uk/prodrg/
> 
>     as reference, and built yourself if necessary.
>      >
>      > Thank you very much!!!
>      >
>      > Best!
>      > Xueming
>      >
>      >
>      >
>      >
>      >
>      > --
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> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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