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, …
[View More]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
>--------------------------------------------
>
>
>
>
>
>
> 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(a)ulb.ac.be
--------------------------------------------
[View Less]
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:
…
[View More]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
--------------------------------------------
[View Less]
