[modeller_usage] model ligand

[Bo Yang <>]

Hello, Modeller:

 

I try to model the ligand into my model by following the example of "Tutorial-2: Modeling ligands in the binding site'. First, I use a template and one of my model to build a alignment of the two. Then manually change the alignment to add "/.." to the end of the structures and sequence in the alignment. And change the number of residues of the structure file in the alignment. I then do the modeling using the modified alignment. But I keep getting the error message:

 

modeller. error: check_a_337E> structure not read in

 

I have checked that the structure files are all in the right path. I don't understand that why Modeller can't read the structure. I notice that the program generated two structure files ( all with xxx_fit) after the alignment. But these "xxx_fit" structures do not include the ligand. If I use these "xxx_fit" structures, there is no error message saying that "structure not read in", instead, it complain that "One or more atoms absent from MODEL". Since there is no ligand residue in such "xxx_fit" files. And if I manually add the ligand residue into the "xxx_fit", again, the modeller can't read the structure anymore.

 

I have included the files used for modeling as attachments. I use mod 8v1.

 

Thank you for help!

 

Bo

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Attachment: 2c17model-ligand1.py
Description: 1426519792-2c17model-ligand1.py

Attachment: 2c17ligand-1b.ali
Description: 4134779604-2c17ligand-1b.ali

 _aln.pos             10        20        30        40        50        60
1PQ2-2C8Ahem  KLPPGPTPLPIIGNMLQIDVKDICKSFTNFSKVYGPVFTVYFGMNPIVVFHGYEAVKEALIDNG 
2c17mul1      ---------------------HMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLI-KK 
2c17          ---------------------HMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLI-KK
 _consrvd                               *    * ***   *  *    *        ** **


 _aln.pos         70        80        90       100       110       120
1PQ2-2C8Ahem  EEFSGRGN--SPISQRITKGLGIISSNG-KRWKEIRRFSL-TTLRNFGMGKRSIEDRVQEEAHC 
2c17mul1      GKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTL 
2c17          GKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTL
 _consrvd                          **        *   **    *                **


 _aln.pos    130       140       150       160       170       180       190
1PQ2-2C8Ahem  LVEELRKTKASPCDPTFILGCAPCNVICSVVFQKRFDYKDQNFLTLMKRFNENFRILNSPWIQV 
2c17mul1      CDMLATHN-GQSIDISFPVFVAVTNVISLICFNTSYKN----GDPELNVIQNYNEGIID--NLS 
2c17          CDMLATHN-GQSIDISFPVFVAVTNVISLICFNTSYKN----GDPELNVIQNYNEGIID--NLS
 _consrvd                  *  *    *  ***    *


 _aln.pos          200       210       220       230       240       250
1PQ2-2C8Ahem  CNN------FPLLIDCFPGTHNKVLKNVALTRSYIREKVKEHQASLDVNNPRDFIDCFLIKMEQ 
2c17mul1      KDSLVDLVPWLKIFP--NKTLEKLKSHVKIRNDLLNKILENYKEKFRS-DSITNMLDTLMQAKM
2c17          KDSLVDLVPWLKIFP--NKTLEKLKSHVKIRNDLLNKILENYKEKFRS-DSITNMLDTLMQAKM 
 _consrvd                        *  *    *                              *


 _aln.pos      260       270       280       290       300       310       320
1PQ2-2C8Ahem  EKDNQKSEF-------NIENLVGTVADLFVAGTETTSTTLRYGLLLLLKHPEVTAKVQEEIDHV 
2c17mul1      NSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQN
2c17          NSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQN 
 _consrvd       **                   *  * * ** ***       *  **  * *  *  ****


 _aln.pos            330       340       350       360       370       380
1PQ2-2C8Ahem  IGRHRSPCMQDRSH-MPYTDAVVHEIQRYSDLVPTGVPHAVTTDTKFRNYLIPKGTTIMALLTS 
2c17mul1      VGFS-RTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWA
2c17          VGFS-RTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWA 
 _consrvd      *                  *   *  *     *   **    *         ***     *


 _aln.pos        390       400       410       420       430       440
1PQ2-2C8Ahem  VLHDDKEFPNPNIFDPGHFLDKNGNFKKSD----YFMPFSAGKRICAGEGLARMELFLFLTTIL 
2c17mul1      LHHNEKEWHQPDQFMPERFLN--PAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLL
2c17          LHHNEKEWHQPDQFMPERFLN--PAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLL 
 _consrvd       *  **   *  * *  **                 ** ** * * ** *** ****     *


 _aln.pos    450       460       470       480       490
1PQ2-2C8Ahem  QNFNLKSVDDLKNLNTTAVTKGIVSLPPSYQICFIPV-----/.. 
2c17mul1      QRFDLEVPDDGQLPSLEGIP-KVVFLIDSFKVKIKVRQAWRE/--
2c17          QRFDLEVPDDGQLPSLEGIP-KVVFLIDSFKVKIKVRQAWRE/.. 
 _consrvd     * * *   **             * *  *