[gmx-users] lipid.itp LJ-1,4 values involving water
lindahl at sbc.su.se
Wed May 3 23:02:22 CEST 2006
They were almost certainly auto-generated from the standard parameters.
On May 3, 2006, at 8:44 PM, chris.neale at utoronto.ca wrote:
> Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values
> lipid atoms and OW or HW? I can understand their inclusion in
> but it seems as if this would never be required in [pairtypes].
> In case anyone else is trying to merge lipid.itp and OPLSAA, here
> is what I have
> done. There is no type of guarantee here, just a listing of what
> appears to be
> working so far for me.
> Download lipid.itp and pope.itp (or your lipid) from
> http://moose.bio.ucalgary.ca/ kindly made available for all by Dr.
> Peter Tieleman.
> 1. Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after
> changing c6/c12
> to sigma/epsilon. Also added atomtype H from olsa_369 to match H
> expected by
> - sigma = (c12/c6)^1/6
> - epsilon = c6/(4*sigma^6)
> 2. Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after
> changing c6/c12
> to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed
> all reference
> to OW to opls_116 (opls spc water oxygen) and simply removed any
> with reference
> to HW as it will be zero regardless.
> 3. Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp.
> - Prior to running ensure that the non-RB dihedral does not exist
> for these
> 4. make a topology file like this:
> #include "ffoplsaa.itp"
> #include "myprotein.itp"
> #include "spc.itp"
> #include "pope.itp"
> [ system ]
> [ molecules ]
> ; Compound #mols
> Protein 1
> POPE 299
> SOL 8991
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