Hi,
I am trying to create two bonds in leap using the script:
source leaprc.ff14SBcirc
addAtomTypes {
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "CE" "C" "sp3" }
}
loadoff parmBSC1.lib
loadamberparams frcmod.parmbsc1
addPdbAtomMap {{OP1 O1P}{OP2 O2P}{H5' H5'1}{H5'' H5'2}{H2' H2'1}{H2'' H2'2}}
set default PBradii mbondi3
dna = loadpdb amber.339t30_newbond.pdb
bond dna.1.P dna.339.O3'
bond dna.340.P dna.678.O3'
savepdb dna check.pdb
saveamberparm dna 339t30.top 339t30.crd
But when I check the output PDB file, no bond has been created.
Could you please advise?
Thanks,
Victoria
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 11 2021 - 14:00:03 PST
