Dear Emilio Lence
Thanks a lot for your reply
Here is my instructions to tleap for ligand parameter generation:
set default PBradii mbondi2
source leaprc.ff99SB
source leaprc.gaff
BP1=loadmol2 BPH-TTR_Ligand1_resp.mol2
loadamberparams BPH-TTR_Ligand1_resp.frcmod
loadamberprep BPH-TTR_Ligand1_resp.prep
check BP1
saveoff BP1 BP1.lib
saveamberparm BP1 BPH-TTR_BP1_resp_nW.prmtop BPH-TTR_BP1_resp_nW.inpcrd
quit
Here is the instructions to tleap for complex parameter generation:
set default PBradii mbondi2
source leaprc.ff99SB
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams BPH-TTR_Ligand1_resp.frcmod
loadamberprep BPH-TTR_Ligand1_resp.prep
loadoff BP1.lib
check
Complex=loadpdb BPH-TTR_Complex.pdb
saveamberparm Complex BPH-TTR_Complex_nW.prmtop BPH-TTR_Complex_nW.inpcrd
savepdb Complex BPH-TTR_Complex_nW.pdb
solvateoct Complex TIP3PBOX 10.0
charge Complex
addions Complex Na+ 0
addions Complex Cl- 0
charge Complex
check Complex
saveamberparm Complex BPH-TTR_Complex_Solvated.prmtop
BPH-TTR_Complex_Solvated.inpcrd
savepdb Complex BPH-TTR_Complex_Solvated.pdb
quit
Can you figure out where the issue it? Please inform me if you require more
information.
Thanks very much!
Cheers
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Received on Thu Oct 15 2015 - 13:30:04 PDT
