[Chimera-users] Error in energy minimizaion - reg

[Eric Pettersen]

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 at 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 at cgl.ucsf.edu <mailto: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 <mailto: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
> <phosphorylated_protein.pdb>_______________________________________________
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