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.lastn...@gmail.com
<mailto:lina.lastn...@gmail.com>> wrote:
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG <yujan2...@gmail.com
<mailto:yujan2...@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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--
========================================
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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