I was trying to simulate a docked complex of peptide and DNA. The DNA .pdb file was developed in Schrodinger and the peptide .pdb files are modelled based on the solution NMR structure in CYANA. After succesful docking, while I loaded the .pdb file of the docked complex in xleap, what I found is "all the atoms in the file are not in residue templates". which is why I encountered fatal errors saying "atoms do not have the type". Earlier I had the same problem but the error was restricted to 4-or 5-atoms, which I could successfully correct according to the nomenclature of xleap. But in this experiments, I had the error for all the atoms in the system. To understand the problem I downloaded another .pdb file from the site and tried to load the pdb in xleap and faced the same issue repeatedly. I apprehend if I am missing some important step while using the .pdb files into xleap. Since I am a novice in the field, I could not successfully troubleshoot the fatal error.
Hi Pallabi,
I suggest two things:
1) Try UCSF Chimera:
https://www.cgl.ucsf.edu/chimera/
File -> open -> your peptide pdb -> save as -> newly named peptide pdb. The protons may need to be deleted before saving.
2) Try antechamber module in AMBER for your peptide. See its manual.
I strongly recommend you should go through AMBER tutorials, before trying them mentioned above:
http://ambermd.org/tutorials/basic/tutorial0/
http://ambermd.org/tutorials/basic/tutorial1/
http://ambermd.org/tutorials/basic/tutorial4b/
Make sure that all residue types, atom names and atom types in the PDB file are defined correspondingly in the force field and molecular fragment libraries that you want to use, and that the format of the PDB file conforms to the convention.
Dear Pallabi..
I have written a MATLAB code.. which will solve all your problems..
Drop me a mail in [email protected]
I can mail you the code and the instructions to use it
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