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

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Wed, 1 Dec 2021 19:09:11 +0000 (UTC)

Dear All,
I want to perform a Thermodynamics integration calculation for calculating the binding affinity between protein and RNA of mutation. The mutation is over a protein sequence from lysine to alanine. The mutation involves converting the residue from 90 to 328. In this PDB 4 ZN ions are present. I have performed parmed command using timerge:
tiMerge :1-238 :239-476 :90 :328

However, It shows the following error:
Merging molecules [:1-238] [:239-476] with sc mask [:90] [:328]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 : 3807 3806 3815 3813). 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 - 3807 3806 3815 3813, three atoms (3807 3806 3813) belong to the RNA whereas the other atom belongs to an amino acid residue of the mutated protein. Please help me out.

Thanks and Regards,
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Received on Wed Dec 01 2021 - 11:30:03 PST
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