[gmx-users] how to restrain four groups!
feenstra at chem.vu.nl
Thu Nov 13 10:45:01 CET 2003
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.
| | |
| _ _ ___,| 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/ |
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