Does anyone have experience using the AlaScan plugin in VMD to make FEP simulation files for alanine scanning?
I keep trying to create the files but I am getting a number of errors: I even used the created PSF file from VMD and it cannot read any amino acids nor gives the output for the FEP simulations.
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file /home/brandon/Desktop/Ala_Scan/equi_VMD/run/equi_VMD_QwikMD-FEP/23-GLU2ALA/mtemp-nprot.pdb
psfgen) Info: pdb file complete.
psfgen) clearing structure, preserving topology and aliases
psfgen) building segment AP1
psfgen) reading residues from pdb file /home/brandon/Desktop/Ala_Scan/equi_VMD/run/equi_VMD_QwikMD-FEP/23-GLU2ALA/mtemp-AP1.pdb
psfgen) extracted 597 residues from pdb file
psfgen) setting patch for first residue to NONE
Alanine scan: Residue GLU 23 of segment AP1 is mutated to E2A
psfgen) mutating residue 23 from GLU to E2A
psfgen) unknown residue type E2A
psfgen) setting patch for last residue to NONE
Info: generating structure...
psfgen) unknown residue type E2A
free(): invalid pointer
Aborted (core dumped)
Hello!, is there any way you upload the pdb file of your protein/peptide which you want to do the mutation?. Perhaps, I can try to build the topology and reproduce the error. Cheers!
Shreya Bhattacharya I was never able to figure it out. I tried all the tips on the VMD forums, but it just kept leading to more errors and my post on the forums went unanswered.
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