[AMBER] Fwd: Creating a bond in leap

From: Victoria E Hill <vehill1.sheffield.ac.uk>
Date: Mon, 11 Jan 2021 21:37:33 +0000

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
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Received on Mon Jan 11 2021 - 14:00:03 PST
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