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(a)ulb.ac.be
>To: modeller_usage(a)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(a)ulb.ac.be
>--------------------------------------------
>
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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: mprevost(a)ulb.ac.be
--------------------------------------------
