[Chimera-users] Error in energy minimizaion - reg

[SELVA BABU SELVAMANI]

Dear Eric,

Here with I am attached the structure I phosphorylated, please kindly help
regarding this.


Thank you!



On Tue, Jan 24, 2023 at 7:01 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Selva,
> I am able to carry out minimization without problem on 1G6G, which has a
> TPO residue.  Does your TPO residue and its adjacent residues have all
> their atoms present?  You might have to send me the structure if that's not
> the problem.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Jan 21, 2023, at 4:29 AM, SELVA BABU SELVAMANI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Developers,
>
> I did phosphorylation of amino acid in protein, then I was about to  do
> energy minimization using Chimera MINIMIZE STRUCTURE module, but it is
> throwing the error ( I mentioned below ).
>
> ****************************************************
> Running PARMCHK for PP.pdb
> Using main parameter file parm10.dat modified by heme-iron.frcmod,
> frcmod.ff14SB, frcmod.ionsjc_tip3p
> *Chimera/MMTK cannot minimize structure, probably because there is no
> parameter for ''No parameters for bond Atom 0.TPO_144__0_0_1_145.N (atom
> type n) - Atom 0.GLN_143__0_0_1_144.peptide.C (atom type C)''*
> **********************************************
>
> *Please help me to sort out the issue.*
>
> I also tried to do phosphorylate using Chimera, even that structure also
> getting the same error while doing energy minimization.
> --
> *Have a nice day,*
> Thanks & Regards,
> *SELVA BABU S*
> M.Sc Scholar (Bioinformatics)
>
> *TNAU, Coimbatore*
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>
>

-- 
*Have a nice day,*
Thanks & Regards,
*SELVA BABU S*
M.Sc Scholar (Bioinformatics)

*TNAU, Coimbatore*
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