While uploading a docked complex (.pdb) onto the PDBsum generation, it shows the following -
Uploaded file contains invalid residue names. Please check that your PDB file conforms to correct PDB conventions.
thanks in advance
Hello Muhammad Adnan Ali,
According to your arrised question, you have wrong file file format for input of PDBSUM (it will only take .pdb extension file for generating any output files). For your convience i have attached the .pdb file below in this comment.
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 View
Hi, I am a third year chemistry undergrad doing my group project in which I need to predict the HPLC retention time of 20 aromatic molecules. to do this we require the chemical properties of these...
24 February 2021 1,384 3 View
I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...
19 February 2021 1,236 1 View
I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...
08 February 2021 7,426 3 View
I have a protein model and want to replace a 12-amino acids-long region within the center of the model with those of a PDB file containing a 12-amino acids long peptide of the same sequence. This...
02 February 2021 779 2 View
I am looking to incorporate a unnatural amino acids which is not available in the swisssidechain database into a protein crystal structure of pdb? I am using chimera 1.14 vis. tool?
26 January 2021 4,064 3 View
I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...
24 January 2021 7,363 3 View
Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...
17 January 2021 843 3 View
Hello everyone, I would like to get help about finding any server or application which can give me info about free energy and dissociation constant of protein-protein docking outputs. I have...
15 January 2021 587 3 View
I have been using PyRx to dock peptides to a protein. Initially the numbers were small so it was okay. But now I have to dock over 500 peptides and doing so manually would take forever. My...
10 January 2021 3,330 4 View