The leaprc.parmCHI_YIL.bsc in AmberTools 1.5 could use some
additional atom mapping to make it more compatible with most PDB files.
--Niel
I think the following version should work in most cases:
---------------------------------------------------------------------------
source oldff/leaprc.rna.ff99
addPdbAtomMap {
{ "H2*1" "H2'1" }
{ "H2*2" "H2'2" }
{ "H2'" "H2'1" }
{ "H2''" "H2'2" }
{ "H5'" "H5'1" }
{ "H5''" "H5'2" }
{ "HO2'" "HO'2" }
{ "HO5'" "H5T" }
{ "HO3'" "H3T" }
{ "OP1" "O1P" }
{ "OP2" "O2P" }
}
addAtomTypes {
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "C3" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "CI" "C" "sp3" }
}
loadamberparams frcmod.parmCHI_YIL
loadamberparams frcmod.parmbsc0
loadoff residues.RNA.parmCHI_YIL.bsc.lib
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Received on Thu Jul 07 2011 - 16:30:04 PDT
