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@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@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* _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
-- *Have a nice day,* Thanks & Regards, *SELVA BABU S* M.Sc Scholar (Bioinformatics) *TNAU, Coimbatore*