[gmx-users] Re: How to use the dummy atom?

[Daan van Aalten]

Hi PeiQuan

If you go to the PRODRG server http://davapc1.bioch.dundee.ac.uk/prodrg
you can draw your molecule in the interactive JAVA-based JME editor and
indicate the chirality of your molecule - you will be given a GMX topology
and starting structure with the correct chirality.

Daan


On Wed, 21 May 2003, PeiQuan Chen wrote:

> Dear gmx-users:
>
> >>        CH3
> >>        |
> >>     Ph-C-OH.       (R.S)
> >>        |
> >>        Dummy atom
> >>
> >> I want to know how to use Dummy atom to represent the molecule.
> >>    Can anyboby give me some hints to how the creat the latter molecular top files? Because I haven't
> >> any experience on use the dummy atoms, I wish you can give me a example top file for it.
> >
> >I don't see that you need dummy atoms. If you use united atoms, there is no
> >hydrogen atom attached to the central Carbon; it will be a 'CH1' atom type,
> >e.g. a Carbon-Hydrogen united atom. You do noeed to add an improper
> >dihedral to keep the right tetrahedral arrangement of the Ph, CH3 and OH
> >groups around the central C. (You'll probably want 2 topologies, one R and
> >one S).
>    Thank you for your help!
>    Yes, I can add an improper dihedral to keep the right tetrahedral arrangement of the Ph,CH3 and OH
> groups arounds the cetral C. But when I want to make a mutation of R-->S or S-->R. How can I  define
> the topology files? Can you help me and give me the topology files.
>    By the way, If I want to add improper diheral to keep, How to define the two different improper dihedral
> in the topology files. Can you give me the topology files?
>    I haven't any experiment on make this type improper diheral! Please help me with a example files.
>
>    Thank you  in advance.
>
> Sincerely yours
> ----
> PeiQuan Chen
> ________________________________________________________________________
> PeiQuan Chen 	Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> gromacs at 163.com
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O