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

PeiQuan Chen gromacs at 163.com
Wed May 21 06:27:03 CEST 2003

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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