Frequently Asked Questions
What are the units of electrostatic potential?How can I visualize the electrostatic potential map in PyMOL?
How can I visualize the electrostatic potential map in VMD?
How long do I have to wait to receive the results?
What happens if the e-mail does not arrive to my e-mail account in a long time?
In which format do the results arrive to my e-mail account?
What can I do if my protein has more than 40000 atoms?
Can I submit protein that are bound to DNA or lipids?
How can I analyze electrostatic potential difference data?
What are the units of electrostatic potential?
APBS writes out the electrostatic potential in dimensionless units of kb*T*ec-1 where
• kb is Boltzmann's constant: 1.3806504 × 10-23 J K-1
• T is the temperature of your calculation in K
• ec is the charge of an electron: 1.60217646 × 10-19 C
As an example, if you ran your calculation at 300 K, then the potential would be written out as multiples of
kb T ec-1 = (1.3806504 × 10-23 J K-1) × (300 K) x (1.60217646 × 10-19 C)-1
= (4.1419512 × 10-21J) × (6.241509752 × 1018 C-1)
= 2.585202 × 10-2 J C-1
= 25.85202 mV
How can I visualize the electrostatic potential map in PyMOL?
Open PyMOL and load the protein PDB file for which you want to visualize the electrostatic potential map.
For this use the PyMOL console, and type the commands shown below.
DirectoryResults is the path on your filesystem to where you have stored the results of your calculations in MutantElec, and protein.pdb is the protein for which you want to visualize the electrostatic potential map.
PyMOL> cd DirectoryResults
open protein.pdb in PyMOL
PyMOL> load protein_map.dx, map
PyMOL> show surface, protein (name only without extension of file)
PyMOL> ramp_new elvl, map,[-2,0,2]
PyMOL> set surface_color, elvl, protein
PyMOL> set surface_solvent
How can I visualize the electrostatic potential map in VMD?
To visualize the electrostatic potential map in VMD, please follow the excellent instructions available at the official web page of VMD: http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/
How long do I have to wait to receive the results?
The calculations usually finish between 20 o 30 minutes from the time they were submitted. However, this could increase if there's a long calculation queue
What happens if the e-mail does not arrive to my e-mail account in a long time?
Check yor Spam folder, or submit the calculations again. You can also contact us if you have further questions with regards to your submitted calculations.
In which format do the results arrive to my e-mail account?
The results are delivered in two formats: online and downloadable for further analysis. In the results email you receive, there are 2 buttons: "View online" and "Download".
•"View online" will take you to a web page in which you can visualize the electrostatic potential maps of the wild type protein against each mutant. Electrostatic potential difference charts are shown, and a message is shown with them, telling you if the differences are statistically significant or not.
•"Download" will start the download of a compressed file. This file contains all the files generated during the analysis if you wish, for example, to perform other analysis or visualize the electrostatic potential maps in PyMOL or VMD.
What can I do if my protein has more than 40000 atoms?
You can delete atoms such as water of ligands (if it has any), or you can split the PDB file
Can I submit protein that are bound to DNA or lipids?
Currently, protein-only calculations are allowed
How can I analyze electrostatic potential difference data?
Since that data is stored in CSV files, you can use any spreadsheet software such as Microsoft Excel or Origin.