Roman,
Could you send me the protein_ala.pdb and protein_thr.pdb files that you used so that I can look into the issue.
Ryan Snyder
________________________________
From: Carlos Simmerling via AMBER <amber.ambermd.org>
Sent: Friday, September 20, 2024 1:00 PM
To: Osman, Roman <roman.osman.mssm.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] An error in TiMerge?
you might need to check directly with Darrin York or his group, they may
not be seeing your message here.
On Fri, Sep 20, 2024 at 12:57 PM Osman, Roman via AMBER <amber.ambermd.org>
wrote:
> Hello,
> I sent the message below about a week ago, and did not receive a response.
> Can someone take a look at it.
> Thanks
> Roman Osman
>
>
> I suspect there is an error in tiMerge.
> I wanted to construct a mutation of a protein and a complex in which an
> Ala is mutated to Thr.
> I created the protein_ala.pdb, protein_thr.pdb and the ligand (h6p).
> I created with tleap the protein.parm7 and protein.rst7 that contain the
> protein_ala.pdb followed by protein_thr.pdb with ions and solvated in a box.
> Similarly, I created the complex.
> Then I ran the tiMerge in ParmEd:
> I get this error message:
>
> ParmEd: a Parameter file Editor
>
>
> Loaded Amber topology file protein.parm7
> Reading input from STDIN...
> > Loading restart file protein.rst7
> > Files are overwritable
> > Merging molecules [:1-760] [:761-1520] with sc mask [:690] [:1450]
> AmberWarning: Molecule atoms are not contiguous! Attempting to reorder to
> fix.
> Action tiMerge failed
> TiMergeError: Cannot have dihedral cross through softcore
> region. (DIHED : 12091 12092 12093 12082). 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.
>
>
> Roman Osman
> Professor
> Department of Pharmacological Sciences
> Icahn School of Medicine at Mount Sinai
>
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Received on Fri Sep 20 2024 - 12:30:02 PDT
