Hello,

Thanks for your prompt answer.

Below is the full input:

from modeller import * from modeller.automodel import * # Load the automodel class

env = environ()

# directories for input atom files

class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='ACE', residues=(self.residues['1:A'])) # self.patch(residue_type='CT3', residues=(self.residues['473:A']))

# Disable default NTER and CTER patches env.patch_default = False

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

a.starting_model= 1 a.ending_model = 1

a.make()

and the error message:

modeller.error: patch___482E> Patching residue identifier not found: ACE

I don't understand the argument for GLUP in noH models. If the total charge of GLUP is zero it should influence differently (compared to Glu -1) the interaction of it with surrounding residues in the construction of the model via the classical part of the force field (Coulomb term)?

Thanks.

Martine.

Forwarded message:

>From: mprevost@ulb.ac.be >To: modeller_usage@salilab.org >Cc: >Date: Wed, 20 Apr 2016 11:31:02 (CEST) >Subject: problem with GluP ACe CT3 patch > >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. > > >-------------------------------------------- > 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: mprevost@ulb.ac.be >-------------------------------------------- > > > > > > > no attachments have been sent > >

-------------------------------------------- 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: mprevost@ulb.ac.be --------------------------------------------