I'm trying to use the ff99SBnmr force field in AMBER 11. When I ask tleap to create the files, it gives lots of errors:
Building topology.
Building atom parameters.
For atom: .R<ILE 2>.A<CG2 7> Could not find type: C3
For atom: .R<LEU 4>.A<CG 8> Could not find type: C4
For atom: .R<ILE 5>.A<CG2 7> Could not find type: C3
(and many more like these)
It looks to me like there's an error in the leaprc.ff99SBnmr file. It specifies the ildn versions of the library files:
loadOff all_amino94ildn.lib
loadOff all_aminoct94ildn.lib
loadOff all_aminont94ildn.lib
But it doesn't include frcmod.ff99SBildn, which defines some of the atom types used in them.
Is 99SBnmr supposed to be based on 99SBildn and include all the parameter modifications in it? If so, then leaprc.ff99SBnmr should include frcmod.ff99SBildn. If not, it should use the non-ildn lib files.
Peter
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Received on Mon Oct 03 2011 - 16:30:02 PDT
