[gmx-users] Topology dihedral or improper dihedral

[lina]

On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <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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