On Jan 23, 2023, at 8:29 PM, SELVA BABU SELVAMANI via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: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.--EricEric PettersenUCSF Computer Graphics LabOn 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 SM.Sc Scholar (Bioinformatics)TNAU, Coimbatore
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--<phosphorylated_protein.pdb>_______________________________________________Have a nice day,Thanks & Regards,SELVA BABU SM.Sc Scholar (Bioinformatics)TNAU, Coimbatore
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