How To Generate Psf File From A Pdb File?
Hi Biostars!
Can someone tell me how to convert a solvated pdb structure with ions to a psf file?
I have tried using VMD but the problem is that it is not taking the water molecules and ions into account, even if the topology file contains information about the ions and water.
I have also tried using charmm gui, but even that dint help me to convert all the information (solvent and ions information) of PDB file to a PSF file.
NOTE: The system is a nucleic acid structure called RNA
Please Help!
• 1,240 views
•
link
updated
by
quentin.delettre
•
written
by
grosy •
•
written
by
grosy •
1 answer
If autoionizer is not working the right way, maybe you can ask/search about it on the vmd mailling list.
• 0 views
•
link
written
by
quentin.delettre
Log in to answer this question.
More posts like this
-
Parameterisation of Metallo-protein with amber
written by Ammar Danazumi •
-
beta-sheet information from pdb file
written by twisted_helix •
-
conversion of DNA sequence to PDB format
written by ashamscsoft •
-
add missing residue
written by lastodin •
-
How To Convert A Simulation Trajectory To A Animation
written by aravind ramesh
-
Getting Started With Nucleic Acid Simulation At The Atomic Level With The Namd Software
written by grosy •
-
Average Torsional Angles Of A Nucleic Acid Structure ?
written by grosy •
-
Perl Script To Calculate All The Nucleic Acid Structure Angles Of A Pdb File
written by Angel •
-
Converting Sdf Format To Pdb Format
written by Tofayel Ahmed •
-
3D Protein Modelling
written by User 0063 •
Where do the ions/solvent come from?
i have added it manually.. but now i want to generate the psf file with all the solvate and ion information in it
Added manually...or by a software/method that place them ? Using automated methods approved by the scientific community is a necessary step when solvating and adding ions. Be careful.
Using the pdb reader from charmm-gui to generate a psf is good and works. Then in your next step (that i assume to use your favorite MD software) you will be able to read the psf and add waters/ions.
well the problem is that VMD is adding the ions out of box(using autoionizer) So, i have used charmm gui to added the ions but to run the ionized file for MD in NAMD, i need the PSF file as well as the ionized file. And the PSF file generated using charmm is not matching with the PDB files after adding ions.