[gmx-users] how to restrain four groups!

[Anton Feenstra]

nanyu101 at sina.com wrote:

> Dear gmx-users,
>  
>   I must restrain the positions of four groups. Would you please give me some advices?
>  
>   I have already done the followings.
> 
> In my topology file:
> include forcefield parameters
> #include "ffG43a2.itp"
> #include "dpp.itp"
> #include "posre_dpp.itp"
> #include "phb.itp"
> #include "posre_phb.itp"
> #include "ions.itp"
> #include "posre_ca.itp"
> #include "posre_cl.itp

This won't work. The position restraints must be part of the molecule
definitions. For 'dpp' and 'phb' it will work as you have it above,
since each .itp file only contains one molecule definition the subsequent
posre*.itp file will be seen as part of that. For the ions.itp, however,
there are a number of ion 'molecules' defined, and your posre_ca/cl.itp
files will only be seen as part of the last ion in ions.itp.

Thus, you will need to #include posre_ca.itp right after the molecule
type definition of CA in ions.itp itself and likewise for CL.



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | 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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