Frequently Asked Questions


Add the parameter --screen=false to your command or screen=false to your config file

After registration, I received login confirmation and accepted the terms of the Licence Agreement , but I am not receiving download emails?

Either you got a mail straight to your junk folder or your TIC department is not allowing FoldX site's emails to pass the filter. Ask them in order to see if you received the email.

How does one uninstall FoldX

FoldX doesn't need to be uninstalled, it is a self-contained binary just delete the executable and the rotabase.txt. For yasara support contact them directly.

Can FoldX model non-amino acid ligands?

Not in thios version, the only residues allowed are here -> http://foldxsuite.crg.eu/allowed-residues

FoldX Suite Download. I have received the registration email but after registering I can not find where to download the suite. I am actually interested in the YASARA plug in.

I am not receiving login confirmation or download emails

Either the email is on your junk or it seems that your company’s mail antispam is rejecting the email. Can you ask your mail server administrator to allow emails from noreply@foldxsuite.crg.es or even from the whole crg.es domain?

what are the units of all these parameters in the output?

All units are given in Kcal/mol

A black windows opens and closes inmediatly

Foldx is not a double click application, you should run it in a command line according to the instrucctions in the manual -> http://foldxsuite.crg.eu/documentation#manual

parametrize, rotabase.txt, new molecule

FoldX uses experimental values for the molecular parameters, so for the moment is not possible to parametrize new molecules. It only uses the entities described below:

http://foldxsuite.crg.eu/allowed-residues

There is any difference between the result of the command "Stability" and the total energy that is shown anytime the program work on a .pdb?

Total energy is equivalent to Stability.

File formats for FoldX

Structures can only be provided as PDB format

installation,foldx, linux

FoldX is a portable executable, there is no need to install it, just run it according to the manual instructions.

The manual pages can be found at: http://foldxsuite.crg.eu/documentation#manual

32 bits applications run in 64 bits systems

Do you guys have updated rotabase.txt file that would contain parameters for sugars and ions? If so, where can one get a hold of it? Thank you!

It comes inside the compressed download file

I try to use the FOLDX. But when I analysed the result, I got confused. (1)Others think that if ΔΔG>0 then destabilize otherwise stablize. I run the program, and ΔΔG=-4.14kcal/mol. Can I think that it stabilize significantly? And I used other predictors,such as I-Mutant 3.0 or i-Stability, the results of ΔΔG<0, and showed it destabilize. If the standard of judge is differrent, in other word, the meaning of "-/+" is different? (2)What is the threshold? 0.5kcal/mol or 1kal/mol?

DDG sign is only a convention, according to thermodynamics a negative DDG implies that your system releases energy achieving a more stable state.

I just tried to use FoldX4, as I have been, but recieved the message "your time has expired. Consider contacting us to extend your license."

Just download a new academic version from the site.

Just download a new academic version from the site.

I have some scripts that call foldx 3b3. Is it possible to download an older version of foldx?

No, it is not possible. Foldx4 is supposed to be the same engine with an improved comand line/config file interface that is easier to use than FoldX3. Adapting the scripts is quite easy, but for any guidance just contact support at javier.delgado@crg.eu

How to introduce retinal parameters in the foldX force field?

The only entities that are supported in foldx are described here:

http://foldxsuite.crg.eu/allowed-residues

Just download a new academic version from the site.

There is no such a thing as a foldx server.

I am trying to use glycosylated molecule to calculate protein-protein interaction energy. sugar-protein interactions could be important. Thank you

No, unfortunately foldx is not able to handle other entities than the ones defined below:

http://foldxsuite.crg.eu/allowed-residues

MacOs plain text file format

Don't save your text files in CR format, for MacOs it is strongly recommended to use LF while saving plain txt files with UTF-8 encoding

-bash-4.1$ ./foldx64Static terminate called after throwing an instance of 'std::runtime_error' what(): locale::facet::_S_create_c_locale name not valid

try to set this before export LANG="C"