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

Anton Feenstra feenstra at chem.vu.nl
Wed May 21 09:28:01 CEST 2003

PeiQuan Chen wrote:
>    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.

I can't give you your topology file, you'll have to make that yourself.
You could use the ProDrg server (search the list archive or use a general
search engine) to get the impropers right, and then adjust parameters to
your liking.

For an example of how to define the improper dihedral yourself, you can
take a look at the rtp entries (e.g. ffG43a1.rtp) of the amino acids,
they all (exept gly) have at least a chiral Calpha with corresponding
improper dihedral. Easiest way to change R to S, is to swap the angle
from positive to negative (alternatively, you can swap two atoms).

By the way, I like to keep the discussions on the list. That way, other
people might benefit from it, too, it gets archived, and possibly if
I get something wrong, somebody else can correct me...!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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