I want to model ONLY magnesium ion (from protein B) on an already crystallized structure (protein A). So the sequence of my target and template is exactly the same. My alignment file is

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>P1;proteinA

structureX:proteinA: 37 :B:+266 :B:::-1.00:-1.00

-QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH*

>P1;proteinB

structureX:proteinB: 401 :A:+1 :A:::-1.00:-1.00

$--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*

>P1;target

sequence:target: : : : ::: 0.00: 0.00

$QYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGEGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH*

when i run this script

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

env.io.atom_files_directory = ['.', '../atom_files']

env.io.hetatm = True

a = automodel(env,

alnfile = 'alignment.ali',

knowns=('proteinA','proteinB'), sequence='target')

a.starting_model= 1

a.ending_model = 1

a.make()

I am getting segmentation fault. Could you please help me?

Regards

Renu