Organic solvent boxes

Due to the demand to use the organic/water mixtures published in the MDMix work done in our group, here you can download two preequilibrated boxes:
  • ETAWAT20 (ethanol 20% concentration)
  • ISOWAT20 (isopropanol 20%). 
These boxes are saved in Amber Object File format. Prepared to work with tLeap or xLeap from Amber software. This program can be downloaded along with the AmberTools (released in Amber website under GPL license  http:// 

If you are familiar with amber software, just load the box in Leap and use it as you would solvate your sistem with any usual water box. For example:

> loadOff 
> solvateOct mysystem ETAWAT20 12.0 iso 1.0     

Other useful comands in tLeap:

- Generate a PDB from the object file (once loaded as before): savePdb ETAWAT20 ETAWAT20.pdb 
- Generate Amber prmtop and prmcrd: saveAmberParm ETAWAT20 ETAWAT20.prmtop ETAWAT20.prmcrd

And if you are using some other software, this object file is ASCII formated and readable (there you have partial charges and all parameters for the atoms). 


AttachmentSize KB
ETAWAT20.off_.gz19.84 KB