Re: [AMBER] Vina Docking model is not accepted in Antechamber

From: Aldo Segura <asegurac666.yahoo.com.mx>
Date: Wed, 17 Oct 2012 07:36:11 -0700 (PDT)

 
Dear Chris,

I mentioned in my first mail that if
you think something is wrong with the connectivity of your pdb file
you should try to send the file to the PRODRG sever. Thus, you can
get a pdb file with “corrected” connectivity and hydrogens,
that's what I did. However, the PRODRG sever incorrectly added a
hydrogen to a nitrogen atom (HBH in your downloaded file), so we get
a wrong bond types. You would delete that atom from the pdb file and
use it on antechamber. I did that and it works!

Best regards,

Aldo

 
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac.ipn.mx; aldosegura.gmail.com
website: www.bioinfolab.org.mx
=========================================


________________________________
 De: Chris Chris <alpharecept.yahoo.com>
Para: Aldo Segura <asegurac666.yahoo.com.mx>; AMBER Mailing List <amber.ambermd.org>
Enviado: Martes, 16 de octubre, 2012 23:09:12
Asunto: Re: [AMBER] Vina Docking model is not accepted in Antechamber
 
Hi Aldo,

Thanks for the structure! Could you tell me what you did? There was an improvement, but alas I obtained the following errors:

cgaughan.tg-login1:~> antechamber -i ctz_101512_100mod1_mod.pdb -fi pdb -o ctz_101512_100mod1_mod.mol2 -fo mol2 -c bcc -s 2
Running: /usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Info: Bond types are assigned for valence state 2 with penalty of 1



Running: /usr/local/packages/AMBER11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 231; net charge: 0
INFO: Number of electrons is odd: 231
      Please check the total charge (-nc flag) and spin multiplicity (-m flag)

Running: /usr/local/packages/AMBER11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/local/packages/AMBER11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

The sqm.out:

--------------------------------------------------------------------------------
  QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons (  165)
QMMM: but odd spin (  1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.

Where did the odd electron come from?

Thanks,
Chris



________________________________
From: Aldo Segura <asegurac666.yahoo.com.mx>
To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, October 16, 2012 3:52 PM
Subject: Re: [AMBER] Vina Docking model is not accepted in Antechamber


Chris,

Try with the attached file. Let me know if it works.

Best regards,


Aldo
 
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac.ipn.mx; aldosegura.gmail.com
website: www.bioinfolab.org.mx
=========================================


________________________________
De: Chris Chris <alpharecept.yahoo.com>
Para: Aldo Segura <asegurac666.yahoo.com.mx>; AMBER Mailing List <amber.ambermd.org>; AMBER Mailing List <amber.ambermd.org>
Enviado: Martes, 16 de octubre, 2012 16:55:02
Asunto: Re: [AMBER] Vina Docking model is not accepted in Antechamber

Thanks Aldo,

I did in fact do this (pdb file attached) but to no avail- 

error:
Warning: detected more than 10 Residue sequence numbers;
    this may be a large multiple residue PDB file;
    large multiple residue PDB files are not supported.
Running: /usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

For atom[10]:O, the best APS is not zero, bonds involved by this atom are frozen

---Judge bond type for Residue 1 with ID of 11 and Name of CTZ ---

Warning: the assigned bond types may be wrong, please : 
(1)
double check the structure (the connectivity) and/or 
(2) adjust atom valence penalty parameters in APS.DAT, and/or 
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time

Error: cannot run "/usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit

basically seems like the same error. Any ideas?

Thanks,

Chris




________________________________
From: Aldo Segura <asegurac666.yahoo.com.mx>
To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, October 16, 2012 1:35 PM
Subject: Re: [AMBER] Vina Docking model is not accepted in Antechamber

Chris,

You should try to use the "pdbqt_to_pdb.py" script included in AutodockTools
(/your_installation/MGLTools-1.5.6rc3/MGLToolsPckgs/AutoDockTools/Utilities24/pdbqt_to_pdb.py). If you think something is lost in your pdb, you could send your ligand pdb fileto The PRODRG Server and download the processed pdb file.

Best regards,
Aldo
 
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac.ipn.mx; aldosegura.gmail.com
website: www.bioinfolab.org.mx
=========================================


________________________________
De: Chris Chris <alpharecept.yahoo.com>
Para: AMBER Mailing List <amber.ambermd.org>
Enviado: Martes, 16 de octubre, 2012 13:47:09
Asunto: [AMBER] Vina Docking model is not accepted in Antechamber

I docked a ligand to a protein using Autodoc Vina. From the resulting .pdbqt file I extracted the model I was interested in, opened it in PyMol, and saved the structure as a .pdb file (see attached). However, when I try to process this .pdb file in antechamber using :

 antechamber -i
ctz_101512_100mod1.pdb -fi pdb -o ctz_101512_100mod1.mol2 -fo mol2 -c bcc -s 2


The following error message is produced:

Warning: detected more than 10 Residue sequence numbers;
    this may be a large multiple residue PDB file;
    large multiple residue PDB files are not supported.
    Continuing, but problems may be encountered.
Running: /usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

For atom[10]:O, the best APS is not zero, bonds involved by this atom are frozen

---Judge bond type for Residue 1 with ID of 11 and Name of CTZ ---

Warning: the assigned bond types may be wrong, please : 
(1) double check the structure (the connectivity) and/or 
(2) adjust atom valence penalty parameters in APS.DAT, and/or 
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be
cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time

Error: cannot run "/usr/local/packages/AMBER11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit

can anyone point me in the right direction here? Should I not use PyMol to make the pdb file? To convert from PDBQT format to PDB format, the simplest thing to do is to remove the charge (Q) and atom type (T) columns but it seems that PyMol has done this....but maybe lost the proper connect data

Thanks,

Chris 
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 17 2012 - 08:00:04 PDT
Custom Search