Thank you for your kind reply. Here is the system details:Protein (1-228 (atom number @1-3621)) 4, Zn (229-232 @3622-3625) ion, ssRNA (233-238 @3626-3814)There is no kind of bond between Protein and RNA. However, this complex formation is stabilized by non-covalent interactions. In the case of normal MD simulation, I have performed up to 2 μs and the complex formation is stable throughout the simulation. Now, I am interested to check the effect of mutation on protein-RNA complex formation using TI. So, I have used the following timerge command:
tiMerge :1-238 :239-476 :90 :328
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,
Saikat
On Thursday, 2 December, 2021, 10:26:03 am GMT-5, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
it might help to tell people more about your system setup. do you expect to
have bonds between the protein and RNA? did everything behave well when you
did normal MD simulations on both endpoints (no TI)?
On Thu, Dec 2, 2021 at 10:07 AM Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> 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,
> Saikat
>
>
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Received on Thu Dec 02 2021 - 08:00:01 PST
