VMD-L Mailing List

From: Brandon Havranek (bjh2_at_uic.edu)
Date: Fri Aug 13 2021 - 23:23:25 CDT

Hello,
I have been trying for a few days now to create FEP files using Alascan and
have been running into a number of issues. More specifically the error
pasted below:

I tried two methods for creating the psf file. One using charmm gui and
then running equilibration to get the xsc file. I then tried using the
QwikMD created psf file and xsc from that simulation. In both cases, the
same error persists. How else do I obtain a correct psf file and run the
simulation to get the xsc file so that I can create the FEP files using
AlaScan? In each case, it seems like it is not recognizing the system as a
host-guest system, even when the option is clicked, as I have not been able
to select residues in one of the chains.

I am not sure where to go from here the same error is persisting even
using other systems. I searched the forums and have not found a solution
either. It seems like the Alascan plugin is no longer functioning
correctly. I tried both the new VMD alpha build and VMD 1.9.3.

psfgen) Info: psf file complete.
psfgen) Info: writing pdb file
/home/brandon/Desktop/Ala_Scan/test/run/test_QwikMD-FEP/358-ILE
ILE2ALA/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/test/run/test_QwikMD-FEP/358-ILE
ILE2ALA/mtemp-AP1.pdb
psfgen) unknown residue type SER
psfgen) unknown residue type THR
psfgen) unknown residue type ILE
psfgen) unknown residue type GLU
psfgen) unknown residue type GLU
psfgen) unknown residue type GLN
psfgen) unknown residue type ALA
psfgen) unknown residue type LYS
psfgen) unknown residue type THR
psfgen) unknown residue type PHE
psfgen) unknown residue type LEU
psfgen) unknown residue type ASP
psfgen) unknown residue type LYS
psfgen) unknown residue type PHE
psfgen) unknown residue type ASN
psfgen) unknown residue type HSD
psfgen) unknown residue type GLU
psfgen) unknown residue type ALA
psfgen) unknown residue type GLU
psfgen) unknown residue type ASP
psfgen) unknown residue type LEU
psfgen) unknown residue type PHE
psfgen) unknown residue type TYR
psfgen) unknown residue type GLN
psfgen) unknown residue type SER
psfgen) unknown residue type SER
psfgen) unknown residue type LEU
psfgen) unknown residue type ALA
psfgen) unknown residue type SER
psfgen) unknown residue type TRP
psfgen) unknown residue type ASN
psfgen) unknown residue type TYR
psfgen) unknown residue type ASN
psfgen) unknown residue type THR
psfgen) extracted 34 residues from pdb file
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE
Info: generating structure...
psfgen) unknown residue type SER
free(): invalid pointer
Aborted (core dumped)