Dear Amber Community,
I am currently working on constructing an Amber force field for a protein containing a lanthanum ion (LA3+), following the guidelines provided in the MCPB.py tutorials (
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php). According to the X-ray crystal structure (pdb: 8DQ2), there are theoretically ten coordination sites on the protein for LA3+, implying that ten coordinate bonds should be established.
However, upon using tleap to generate the topology and coordinate files using the command "tleap -s -f 8DQ2_tleap.in > 8DQ2_tleap.out," I have encountered an issue. It appears that only first eight coordinate bonds have been successfully constructed, with the 9th and 10th bonds failing to form. The leap.log file indicates the following:
> bond mol.60.OD1 mol.111.LA
> bond mol.62.OD1 mol.111.LA
> bond mol.62.OD2 mol.111.LA
> bond mol.64.OD1 mol.111.LA
> bond mol.64.OD2 mol.111.LA
> bond mol.66.O mol.111.LA
> bond mol.68.OE1 mol.111.LA
> bond mol.68.OE2 mol.111.LA
> bond mol.71.OE1 mol.111.LA
Bond: Maximum coordination exceeded on .R<LA1 111>.A<LA 1>
-- setting atoms pert=true overrides default limits
> bond mol.71.OE2 mol.111.LA
Bond: Maximum coordination exceeded on .R<LA1 111>.A<LA 1>
-- setting atoms pert=true overrides default limits
Upon inspection using VMD, I confirmed that there are only eight coordinate bonds to the metal ion present in the topology file.
I attempted to address this issue based on the warning message by adding the line "set mol.111.LA pert true" separately, but unfortunately encountered the same problem:
GU2 = loadmol2 GU2.mol2
LA1 = loadmol2 LA1.mol2
loadamberparams frcmod.ionslm_126_opc
loadamberparams 8DQ2_mcpbpy.frcmod
mol = loadpdb 8DQ2_mcpbpy.pdb
set mol.111.LA pert true
bond mol.60.OD1 mol.111.LA
bond mol.62.OD1 mol.111.LA
bond mol.62.OD2 mol.111.LA
I kindly request your assistance in resolving this issue. Attached are the relevant files.
Warm regards,
Zhenyue.
==============================================================
Zhenyue Yang
Assistant Professor
Northeast Normal University - Frontier Interdisciplinary Research Institute
Email: zyyang666.nenu.edu.cn
Address: Renmin Street No 5268, Changchun 130024, P.R. China
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Received on Sun Mar 17 2024 - 04:30:02 PDT
