Hi all,
I would like to prepare. prmtop and. inpcrd for my ligand-Metalloprotein complex (protein + ligand+ 2*Zn/Cl/Ca ions). I have prepared .lib files for Zn2+ and Ca2+ as explained (
https://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.php) by AMBER-14. I tried loading the atomic_ions.lib and different combinations of amber residue name and corresponding atom type for a chloride ion (CL/Cl-, Cl-/ Cl- and so on) in the pdb input file, but that doesn't seem to work and still there is an issue for reading chloride ion:
FATAL: Atom .R<Cl- 700>.A<CL 2> does not have a type.
Can anyone help me with this?
I appreciate any help/suggestion
Zahra
#### load the AMBER force fields
source leaprc.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadoff /home/zahratehrani7/atomic_zinc.lib
loadoff /home/zahratehrani7/atomic_cal.lib
loadoff atomic_ions.lib
NEW_parm = loadamberparams lig-WithH.parm
loadamberprep lig-WithH.prep
mol = loadpdb xray_prep.pdb
check mol
savepdb mol 02_complex.pdb #Save the pdb file
saveamberparm mol 02_complex.prmtop 02_complex.inpcrd
quit
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Received on Sun Aug 01 2021 - 00:00:02 PDT
