[Chimera-users] MMTK/Chimera interface error

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 27 14:29:28 PST 2017


> On Feb 26, 2017, at 1:07 PM, ADIL AHIRI <ahiri.adil at gmail.com> wrote:
> 
> hi everyone,
> 
> I work on the modeling of the effect of phosphorylation on segment peptide.
> 
> I had a problem when i use this interface MMTK/Chimera interface because when i use a doubly phosphorylated peptide i have this message:
> 
> KeyError: 'No parameters for bond Atom 0.ARG_12__0_0_1_286__B.peptide.C (atom type C) - Atom 0.TPO_13__0_0_1_287__B.N (atom type n)'
> 
> You will find attached a sample problem source file.
> 
> Is there anyone who can help me solve this problem please.

Hi Adil,
	There are various obstacles to minimizing your structure.  The specific problem above is that Chimera doesn’t know to generate the missing inter-residue forcefield parameters between the non-standard TPO residues and their neighboring standard residues.  The solution is to change the TPO backbone atom types from their antechamber-assigned GAFF atoms types to the corresponding regular AMBER atom types (c->C; n->N; c3->CX).
	First you should work from the attached modified file that Elaine Meng created where truncated residues in your structure are changed to alanine.  Then execute the following commands to add hydrogens, remove one spurious hydrogen, add charges and atom types, change the atom types I mentioned, and then minimize:

addh
delete @h2p
addcharge
setattr a gaffType CX :TPO at CA
setattr a gaffType C :TPO at C
setattr a gaffType N :TPO at N
minimize

	Eric Pettersen
	UCSF Computer Graphics Lab


-------------- next part --------------
A non-text attachment was scrubbed...
Name: fixfile.pdb
Type: application/octet-stream
Size: 22008 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170227/a8214982/attachment-0001.obj>


More information about the Chimera-users mailing list