[gmx-users] FEP

[Michal Kolinski]

Hi all.
1)

Thank you all  for comments and help on FEP issue. 
  I still have problems with setting up the system. 
How can I obtain topology for DPPC lipids to use with GROMOS96 
force field for protein membrane simulations.  Should I 
stay with old ffgmx force field, is it the best choice.
Is it possible to adopt old lipid parameters (lipid.itp
 for ffgmx) for new GROMS96 force field. 

2)

During FEP calculations I need to 
slowly turn off charges and LJ interactions for Zn2+ ion.
In my dual topology for Zn2+ I have:

  
[ moleculetype ]
; molname       nrexcl
ZnB              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge              typeB chargeB massB
1       Zn      1       Zn              Zn       1      2     65.37000      Zn (?)    0  0

and that will only perturbate charges on the Zn atom. 
 In order to turn off  Zn ion  LJ interactions I need to 
change it into dummy atom.   I'm using ffgmx forcefield and
 which atom type should I use for above Zn(?).   I checked 
ffgmx.atp and there is no atom type DUM (like in GROMOS96).  
 Does it mean I have to add new atom type DUM in all ffgmx.atm,
 ffgmxnbon.itp..  files.   Please give my some suggestions. 
Thank you for your time and help.
All best.
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