[AMBER] TiMergeError: Cannot have dihedral cross through softcore region

From: Jissy Akkarapattiakal Kuriappan <Jissy.Kuriappan.iit.it>
Date: Wed, 30 May 2018 13:07:15 +0000

Hi all,



  I am preparing systems for a FEP calculation in AMBER. I have a protein-DNA system with a bound (non-covalent) drug molecule. I want to perform calculations by mutating two consecutive residues, MET-SER to GLN-ALA. In order to generate correct topologies and coordinate files, in accordance with the tutorial given - http://ambermd.org/tutorials/advanced/tutorial9/#sidechain_mini , I used tiMerge. I could create the files for my system without the bound ligand . However when I try to do the same for my system with the bound ligand, I get the following error:



Merging molecules [:1-1551] [:1552-3102] with sc mask [:327-328] [:1878-1879]
AmberWarning: Molecule atoms are not contiguous! I am attempting to reorder the atoms to fix this.
Action tiMerge failed
    TiMergeError: Cannot have dihedral cross through softcore region. (DIHED : 25797 25818 25820 25800). Usually this means you have defined the softcore region in a way that breaks a ring. Try redefining your softcore region to include the ring or at least three consecutive atoms.


Of the 4 atoms which are pointed at in the error - 25797 25818 25820 25800, two atoms belong to the ligand whereas the other 2 atoms belong to an amino acid residue. The ligand forms no covalent bonds to the protein and is about 20 away from the amino acid residue pointed to in the error. Can someone please help me resolve this problem?

Thanks in advance.




Best Regards,

Jissy A. K., PhD

Marie Curie Post-Doctoral Researcher

Drug Discovery and Development

IIT - Italian Institute of Technology

Via Morego 30, 16163 Genova - Italy


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Received on Wed May 30 2018 - 06:30:02 PDT
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