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

David spoel at xray.bmc.uu.se
Wed May 21 08:24:01 CEST 2003

On Wed, 2003-05-21 at 06:26, 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.
put your molecule (the above drawing) in the prodrg server and check the
topology for one molecule. Then find the improper you need to change.
Going from R->S probably means just modifying the sign of the angle in
the improper, so that would be

A B C D 1 -35 160 35 160

check manual chapter 5 and turn on free energy stuff.

>    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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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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