Dear Amber Users,
I have a protein with a nonstandard residues, a phosphotyrosine, which I
called TYS. I generated the mol2 file using the program RESP ESP charge
Derive [
http://q4md-forcefieldtools.org/RED/ ] The I used antechamber to
get a formated mol2 file and parmchk to get a frcmod file. The lib file was
obtained using tleap.
Loading my protein in tleap is working and the TYS residue is recognized,
however I got the following warning for all non-recognized atoms.
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CA-N-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
Finally I have trouble when I try to save the prmtop and prmcrd files.
Below is the error. Can anyone please help out?
I checked also the mailing list, people have reported this error. Thanks
so much for your help.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - n3
Could not find bond parameter for: c1 - N
Could not find bond parameter for: C - n3
Could not find bond parameter for: c1 - N
Building angle parameters.
Could not find angle parameter: O - C - n3
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - c3
Could not find angle parameter: CT - C - n3
Could not find angle parameter: o - c1 - N
Could not find angle parameter: c1 - N - H
Could not find angle parameter: c1 - N - CT
Could not find angle parameter: c3 - c1 - N
Could not find angle parameter: O - C - n3
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - c3
Could not find angle parameter: CT - C - n3
Could not find angle parameter: o - c1 - N
Could not find angle parameter: c1 - N - H
Could not find angle parameter: c1 - N - CT
Could not find angle parameter: c3 - c1 - N
Building proper torsion parameters.
** No torsion terms for O-C-n3-hn
** No torsion terms for O-C-n3-hn
** No torsion terms for O-C-n3-c3
** No torsion terms for C-n3-c3-h1
** No torsion terms for C-n3-c3-c3
** No torsion terms for C-n3-c3-c1
** No torsion terms for CT-C-n3-hn
** No torsion terms for CT-C-n3-hn
** No torsion terms for CT-C-n3-c3
** No torsion terms for o-c1-N-H
** No torsion terms for o-c1-N-CT
** No torsion terms for c3-c3-c1-N
** No torsion terms for h1-c3-c1-N
** No torsion terms for c3-c1-N-H
** No torsion terms for c3-c1-N-CT
** No torsion terms for n3-c3-c1-N
** No torsion terms for O-C-n3-hn
** No torsion terms for O-C-n3-hn
** No torsion terms for O-C-n3-c3
** No torsion terms for C-n3-c3-h1
** No torsion terms for C-n3-c3-c3
** No torsion terms for C-n3-c3-c1
** No torsion terms for CT-C-n3-hn
** No torsion terms for CT-C-n3-hn
** No torsion terms for CT-C-n3-c3
** No torsion terms for o-c1-N-H
** No torsion terms for o-c1-N-CT
** No torsion terms for c3-c3-c1-N
** No torsion terms for h1-c3-c1-N
** No torsion terms for c3-c1-N-H
** No torsion terms for c3-c1-N-CT
** No torsion terms for n3-c3-c1-N
Building improper torsion parameters.
total 604 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
--
Cheers,
Paul
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Received on Mon Oct 29 2012 - 07:30:04 PDT
