Hello,
I prepare a protein prmtop file using tleap with current bug-fixed AmberTools15.
I obtain different results using the commands below:
source leaprc.ff10
prot = loadPdb prot.pdb
saveAmberParm prot prot.top prot.crd
or
source leaprc.ff99SB
prot = loadPdb prot.pdb
saveAmberParm prot prot.top prot.crd
I understand that the CA is now CX rather than CT but it should not change bonded force constants and equilibrium values?
In case of using the ildn modifications with 'source leaprc.ff10' would give very different prmtop but:
source leaprc.ff99SB
loadamberparams frcmod.ff99SBildn
loadOff all_amino94ildn.lib
loadOff all_aminoct94ildn.lib
loadOff all_aminont94ildn.lib
or
source leaprc.ff99SBildn
give almost the same prmtop except the modified Bondi radii - I wonder where these radii are stored for leap and why the new ildn atom types changed those.
I note that I do not see the latest OL modifications for RNA in ff10 in contrast to what is in the manual.
Any insight would be appreaciated.
Peter
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Received on Tue Jul 26 2011 - 14:30:03 PDT
