[gmx-users] LJ-14 interactions in lipid.itp

Semen Esilevsky yesint4 at yahoo.com
Mon Jun 14 16:36:55 CEST 2004

Dear All,
Probably my question was already discussed but...
I'm constructing the sistem of DMPC mambrane and the
small probe submerged to the membrane. The probe has a
rather long hydrocarbon tail. I want to apply
optimized parameters from lipid.itp to this tail. What
I did is just change CH2 to LP2 and CH3 to LP3 and
make a .rop file like this:

#include "ffgmx.itp"
#include "lipid.itp"
#include "f2n8.itp" ;it's the probe

#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ system ]
; name

[ molecules ]
; name	number
DRG    1  ;only the probe so far

Thare are two questions:
1) When I fed this to grompp it complaint about
duplicate defaults in lipid.itp. Should i just remove
[defaults] directive from lipid.itp or some other
procedure is preferable?

2) If I remove defaults from lipid.itp it starts to
produce warnings about missed default LJ-14 parametres
for all LP2-CH2 LP3-CH2 and the like. Why? All this
pairs are present in lipid.itp and it is included
before my topology ?! I can just add these LJ params
by hand, but I'm not sure that it is a correct way.

Please give me some hints.

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