[modeller_usage] fwd:problem with GluP ACe CT3 patch

[Prevost Martine <>]

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: 
>To:   
>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: 
>-------------------------------------------- 
> 
> 
> 
> 
>
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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: 
--------------------------------------------