Dear experts,
I am trying to prepare a protein-DNA-copper complex, regarding the metals, a Cu+2 and Mg+2 are included in my input pdb, I followed the instructions of tutorial 20 for the non-bonded metals, obtained a CU.lib file, loaded it as loadoff CU.lib and worked on tleap. But then, I removed this line which is reading the CU.lib, and still tleap works….
I am puzzled here, I thought this CU.lib is necessary for tleap to obtain the right parameters of this specific Cu+2 metal type. I am probably wrong?
Why is then still working without the library file?
Is the tip3p force field including those parameters for Cu+?
Am I doing something completely wrong?
This is my input file, as I said it works with or without the loadoff lines for CU or MG (both of them in my pdb).
Thanks!!
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff
source leaprc.DNA.OL15 # DNA force field
source leaprc.phosaa10 # Parameters for phosphorylated amino acids
set default PBradii mbondi3
loadAmberParams frcmod.ionsjc_tip3p # Joung/Cheatham ion parameters for TIP3P water
loadoff CU.lib
CU = loadpdb CU.4amber.pdb #Load the PDB file
loadamberparams FC5_SP2.ante.frcmod
LIG = loadmol2 FC5_SP2.ante.mol2
REC = loadpdb 2XKK.clean.3.pdb # load PDB REC
loadoff MG.lib # MG library
COM = combine {REC LIG CU}
savepdb COM 2XKK.tleap.COM.dry.pdb
saveamberparm COM 2XKK.tleap.COM.dry.prmtop 2XKK.tleap.COM.dry.rst7
Best,
Fabian
Fabian Glaser PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
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Received on Thu Jun 13 2019 - 08:30:02 PDT
