QligFEP automatically generates runCLUSTER.sh within inputfiles. The problem is that generated run.sh always contains:

time mpirun -np 32 $qdyn eq1.inp > eq1.log (for example)

which will run for example on CSB, but not on Tetralith where mpirun should be replaced with mpprun

it can be replaced manually with sed -i 's/mpi/mpp/g' run.sh but it is not really convenient if there is a lot of molecules.

Virtual sites generate erroneous definition of the corresponding dihedrals; lines 432-433 and 449-450 need come addition (I have the code but I am null on github) ;-)

Hello,
Sorry to bother, I'm trying to repeat the CDK2 example in the tutorial folder by following the instructions in the Readme.md. In the third step of seting up FEP, after executing python setup.py, the following error occurs:

 usage: QligFEP [-h] -l1 LIG1 -l2 LIG2 -FF {OPLS2005,OPLS2015,AMBER14sb,CHARMM36,CHARMM22,CHARMM_TEST} -s {water,protein,vacuum} -c CLUSTER [-r SPHERERADIUS] [-b CYSBOND] [-l {1,0.5}] [-T TEMPERATURE] [-R REPLICATES]
               [-S {linear,sigmoidal,exponential,reverse_exponential}] [-w WINDOWS]
QligFEP: error: argument -b/--cysbond: expected one argument

The error is caused by the line 98 in setup.py call = setupFEP + ' -l1 ' + mol1 + ' -l2 ' + mol2 + ' -FF OPLS2015 -b' + cysbond + ' -S sigmoidal -s protein -c TETRA -r 25 -l 1 -w' + windows , where the option -b is empty. I checked the protPREP.log in 2.protprep in which no s-s bond is crearted for this protein. And if I removed the '-b' option, no error would occur. So Is there an 'if condition' missed in the setup.py so that proteins with no S-S bond don't need '-b' option.

Thanks

Hi, first of all thank you so much for your amazing work in putting this together along with the documentation and tutorials, they helped me a lot.

I am running the FEP tutorial, and everything seems to be working. I have successfully completed the water leg of the simulations and I have been running the protein leg for 12+ hours on my unis cluster (using 32 cores per each of the 10 jobs).

I was wondering if there was a way to monitor what stage the job is currently in (i.e., eq. or which of the md stages) or some sort of performance metric, so I can track how long it will take to run. The files in my FEP1/298/[1-10] have not updated since submitting the run, but my slurm_[x].log shows no errors and the jobs are apparently running exactly as they did for the water simulations (although that was much faster, naturally).

@edit: I just figured out I was using the wrong MPI version in the protein simulation, so the software was not even running. Using the right MPI version allows me to track the files being updated in the folder. Sorry for the confusion!

Thank you again

Hello,
Could you add a tutorial of simulating GPCR proteins ? In the second step of preparing proteins, protprep.py can't recognize lipids (in my case POPC lipids prepared in Charmmgui) and therefore no protein.pdb is produced. Also, since membrane MD/FEP simulation involves anisotropic coupling of pressure ,in XY and Z direnction, is the third step(set up FEP) also different from CDK2 example? Thank you.