Dear All
I've been reading several mails that adress the problem of acetylated N-termini
when refining peptide ligands with refmac. I managed to include LINKR records
after running refmacs "review restraints" as suggested by Eleanor Dodson in one
of the mails I found:
LINKR C ACE I 0 N TRP I 1 ACE_C-N
But the records themself are obviously not sufficient to maintain the ACE
linked to TRP during refinement and ACE moves away.
Eleanor Dodson wrote about that topic:
"If you run [...] review restraints, it will detect and make a LINK entry for
you
Then you will need to use the GUI task - merge monomer library to combine your
corrected MAL with the new LINK
Run refmac again with XYZIN the output from "review restraints " task (that
will include a LINK record) and it should/might! work..."
If I read that correctly, Review restraints should produce a LIBOUT that can be
loaded as .cif in a later step for refinement? Such a file was
not produced.
I tried afterwards:
1) To regularize and safe an ACE-TRP monomer in JLIgand and load the .cif as
LIBIN for refmac. The link is found, but ACE still moves away with
the same messages:
WARNING : link:ACE_C-N is found dist = 1.361 ideal_dist= 1.329
ch:II res: 1 TRP at:N .->Ia res: 0 ACE
at:C .
Even though XYZOUT still contains the LINKR records.
2) As I suspected, refmac needs except for the LINKR record a LIBIN that should
be produced when running Review Restraints. As this .cif file
is not produced, I sent the whole ligand to prodrug and safed the .cif from
there. But that did not work out either.
3) I also tried to change the LINKR record into LINK
I failed until now to tell refmac to maintain ACE linked to the TRP. I know
this issues have been discussed before, but none of the suggestions helped yet.
Any help would be highly appriciated.
