Error in energy minimizaion - reg
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*
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
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*
Hi Selva, Your structure minimizes without error for me. Instead of going back and forth on the mailing list, can you use Help→Report A Bug in Chimera to submit a bug report? That will provide me with a lot information, such as the version of Chimera you're using, what platform you're on, etc. without me asking a bunch of questions or guessing. Thanks! --Eric
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 <mailto: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 <mailto: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 <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
-- Have a nice day, Thanks & Regards, SELVA BABU S M.Sc Scholar (Bioinformatics) TNAU, Coimbatore <phosphorylated_protein.pdb>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
SELVA BABU SELVAMANI