AMBER Archive (2005)

Subject: AMBER: 10-12 potential and create atom type

From: Fabien CAILLIEZ (Fabien.Cailliez_at_ibpc.fr)
Date: Thu Jun 30 2005 - 12:19:41 CDT

Dear AMBER users,

I would like to create a new atom type, which would have those features :
- no 6-12 interactions with protein atoms.
- 10-12 interactions with water oxygen atoms.

Here is what I have tried :
source leaprc.ff99
addAtomTypes { {"GR" "Mn" "sp2"} }
i = createAtom CAG GR 0.0
set i element Mn
set i position { 0 0 0 }
r = createResidue CGI
add r i
CGI = createUnit CGI
add CGI r
loadAmberParams frcmod
mol = loadPdb inp.pdb
savepdb mol outleap.pdb
saveAmberParm mol outleap.top outleap.crd
quit

And here is my frcmod :
remark goes here
MASS
GR 100.0

HBON
  GR OW 0.300 0.0000

NONBON
  GR 0.000 0.0000

It seems that the HBOND part is not used by Leap. I tried to remove the
part about NONBON, but Leap wants it to be here (it says: Modified force
field files must contain both a MASS and NONB entry, or neither).

Does my problem can be solved with Leap ?

Thamk you in advance for your help,
Fabien
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