I am trying to model point mutations in protein structures in Yasara using the FoldX plugin but I always get the same error: "Cannot read FoldX RepairPDB output". This is apparently a known error and I have followed the troubleshooting section in the Yasara manual but to no avail.
I am using Windows 8, Yasara version 16.4.6 and I have the latest version of FoldX (downloaded today). I have provided Yasara with permissions to write to its own directory (Full control via the Yasara>Properties>Security), I have updated the FoldX license and I am using a pdb file on which I have worked previously in Yasara on this computer.
This is a problem that comes back yearly with every FoldX license update and usually solves itself by fumbling around with the files but I'm unable to get it to work this time.
I've run out of ideas and would be happy to hear any suggestions or comments from you on what is causing it and how to solve it.
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Error message:
>LoadPDB D:\Protein modelling\protein.pdb - Model 1 loaded as object 1 (4358 atoms)
>RunPlugin foldx.py - OK
>StopPlugin - OK
>RunPlugin foldx.py - OK
>Console Flag=Hidden - OK
>ListRes Property=10000 - OK
>ListMol Obj 1,Format=MOLNAME - OK
>SavePDB 1,Filename=F:\Programs\yasara\plg\foldx_cache\Object1.pdb - OK
>ShowMessage Text="Repairing Object 1. This can take a few minutes. Please cite Van Durme et al., Bioinformatics. 2011 Jun 15;27(12):1711-2" - OK
>LoadPDB Filename=F:\Programs\yasara\plg\foldx_cache\RepairPDB_Object1.pdb - ERROR - File F:\Programs\yasara\plg\foldx_cache\RepairPDB_Object1.pdb not found.
>HideMessage - OK
>RaiseError Text="Cannot read FoldX RepairPDB output. Please see the troubleshooting section at http://foldxyasara.switchlab.org" - ERROR - Cannot read FoldX RepairPDB output. Please see the troubleshooting section at http://foldxyasara.switchlab.org.
For anyone who might be interested, it seems there were 2 different problems:
There are compatibility issues between the current version of FoldX and the old Yasara/FoldX plugin (available from the Yasara website), which is why you need the new Yasara/FoldX plugin (available on the crg website) together with the current version of FoldX. However, the Yasara/FoldX plugin is recognized by Python 2.x but not by Python 3.5. I uninstalled Python 3.5 and went back to a 2.7 version, which then allowed the new Yasara/FoldX plugin to be recognized together with FoldX.
Second, when configuring the foldx.exe and rotabase.txt files, I kept getting the same error and figured out that it's because the path to these files contained spaces. I moved the files to a folder where there were no spaces (i.e. D:/Protein models/ to D:/Protein_models/) and the problem was finally solved.
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