Hello everyone
I need to dock a protein with some 5 ligands.structures of the four ligands were downloaded from pubchem,where the last one from PDB. I used prodrg server for energy minimization of the ligands.
1.The last one which was downloaded from PDB showed an error shown below:
PRODRG> Starting up PRODRG version AA100323.0717
PRODRG> Parameter set 'pd/gromos96' (fftype=2).
PRODRG> PDB mode detected.
PRODRG> C1 is bonded to C2 O1 O5 C1 C2 N O1
ERRDRG> Atom with more than 4 connections.
PRODRG> Program terminated unsuccessfully, sorry!
2.Also for the other 4 energy minimized ligands,the output folder contained many files in the PDB format,in the mol2 format and in TOP format.Which one should be used for docking.
3.For a trial run I randomly selected one PDB file from the output folder.After docking with the protein,the binding enrgy before and after energy minimization are almost same but,interacting partners are a little different.What does it imply?
Hi waqar
I am using Hex for docking and for minimization online server prodrg.
You can use autodock for ligand minimization and docking. Its free.
Hi Shreyasi Asthana,
Many online and offline tools and software available which used the different algoritham. prodrg is good tool but you also Swiss-pdbviewer 4.1.0 or also a commercial software yasara which is very good energy minimized the ligands and also the protein molecules.
hi,
Try energy minimization with arguslab or autodock !!
For the second question, you can consider any format for docking according the input format for your docking program.
For the third one, Change in the interacting residues may be because of the torsion change during the energy minimization. Inorder to confirm that try docking with ligand (Befor energy minimization) for two times and see the interacting residues are same for those two results .
Hi,
Try autodock for energy minimization. You can try also under Amber FF instead of gromos.
What is your ligand? Because Hex was design for Prot-Prot docking and Prot-DNA docking. In other case, better to use another tool : autodock, swissdock, Zdock, DOCK, ...
Trust this help.
@Aurore
My ligand is heparin.The structure is available from PDB.Code is H1PN.Do all the energy minimizations yield somewhat diffrent results?
Yes!!! There a random seed for each energy minimisation.
For your ligand, if you still have trouble, you can try antechamber to get the parameters for the ligand.
Trust it help.
@Aurore
Chimera uses antechamvber for energy minimization,I guess.When I tried with chimera it also shows an error message.With all the other ligands both prodrg and chimera fine.Only this particular ligand(PDB code:1HPN) shows error meaasge.
Hi, I don't really how antechamber is working in chimera. But you can use it in command line.
What is exctly the error?
Dear I checked the pdb file. Did you gave it like this to PRODRG ? Because there is 2 model. Select one, save it in a PDB file and try again.
Trust this help
Hi,
optimize or energy minimize the selected ligands using SwissPDB viewer or Vegaz software or Chemdraw program. Swiss pdb viewer would provide energy minimization value for the ligands. then it is useful to carry out further experiment.
thanks
Rajesh
The theory of energy minimization before docking is just to remove clashes among atoms of the ligand and to develop a reasonable starting pose. Every docking software used this minimized docking pose of the ligand and perform conformational search using their own algorithm.
The easy way to get the minimized ligand conformation is to use a software called Avogadro http://avogadro.cc/wiki/Main_Page which can able to minimize the ligand using a several force fields such as GAFF, UFF, MMFF94, MMFF94S etc. with either steepest descent or conjugate gradients algorithm. This software is free and is reasonably well used for docking based ligand minimization. You can save your minimized ligand in several number of formats.
In case of minimization of protein to remove bad flips and correct protonation I would suggest you to use H++ server. You can use the output PDB from the server for docking. If there is p[roblem with some flipping residues you can adjust them manually or you can try AMBER or Gromacs to perform a small minimization in order to remove the clashes and bad flips.
Hope it helps,
SB
https://www.researchgate.net/profile/Samee_Ullah2
Can u plz suggest me after minimize energy through Avogadro then which steps we follow to convert ligand in pdbqt and how Avogadro convert structure in 3D
Hello Shreyasi Asthana
Energy minimization is crucial during your in silico works, because, PDB doesn't evaluate the structures it receives, for errors. This paper will help you understand that:
DOI: 10.1038/343687a0
There are many online servers that can do this work for us, out of which, I shall recommend you 3 of the best energy minimization servers available for use, accounting the fact that, they are being used by many researchers in their works:
• Moderefiner:
http://zhanglab.ccmb.med.umich.edu/ModRefiner/
• Yasara:
http://www.yasara.org/minimizationserver.htm
• Chiron:
https://dokhlab.med.psu.edu/chiron/processManager.php
Hope it helps.
Johnson Samuel sir i am not able to save my pdb structure through yasara. it will not show the pdb file in that folder.
Hello Pallavi Agrawal
I'm attaching the link to Yasara's guide. Navigate to chapter 3.6, and you have clear explanation of how to troubleshoot your problem.
https://ceberndsen.github.io/YASARA-guide/
Hope it helps.
Thanks Soumendranath Bhakat . I downloaded this tool from Avogadro but not able to draw structure in it. It is not that friendly as other structure drawing tools are. May I know if I can use .cdx file in some of the energy minimization software as input file?
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