Hi,
They were almost certainly auto-generated from the standard parameters.
Cheers,
Erik
On May 3, 2006, at 8:44 PM, [EMAIL PROTECTED] wrote:
Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values
including
lipid atoms and OW or HW? I can understand their inclusion in
[nonbond_params],
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
pope.itp
- 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
groups.
4. make a topology file like this:
#include "ffoplsaa.itp"
#include "myprotein.itp"
#include "spc.itp"
#include "pope.itp"
[ system ]
system_name
[ molecules ]
; Compound #mols
Protein 1
POPE 299
SOL 8991
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