[modeller_usage] problem with GluP ACe CT3 patch

[Prevost Martine <>]

hello,

I am trying to patch a protonated glu as well as ACE and CT3.
Most of the documentation on patches is for DISU.
As for ACE or CT3 (which is what I tried first) I used:

class mymodel(automodel):
    def special_patches(self, aln):
        self.patch(residue_type='CT3', residues=(self.residues['473:A']))

a = mymodel(env, alnfile = 'all.pir',
              knowns = ('3ob6_A','3ob6_B'),
	      sequence = 'Can1_E184H')

a.starting_model= 1
a.ending_model  = 1

I got the following error:

patch___482E> Patching residue identifier not found:  CT3

Same thing for ACE. I also tried with allhmodel but it fails as well.

Another question for GLUP patching in no hydrogen models how can one be sure that one got indeed GLUP?

Thanks in advance for your help,

Martine.


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  Martine Prévost
  Structure et Fonction des Membranes Biologiques 
  CP 206/2
  Université Libre de Bruxelles
  Bld du Triomphe
  B-1050 Bruxelles
  Belgium
  Phone : 32-2-650 2049
  Fax   : 32-2-650 5382
  E-mail: 
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