(VMD) 1 % autopsf -mol MOLID
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: MOLID
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
expected integer but got "MOLID"Not valid molecule id MOLID in atomselect's 'molId'
>Main< (VMD) 2 % -protein
invalid command name "-protein"
>Main< (VMD) 3 % autopsf -protein
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
Need to have at least one atom in your selection!
>Main< (VMD) 4 % autopsf -nucleic popc128a.pdb
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: false osel: protein or nucleic nfrag: true
Need to have at least one atom in your selection!
>Main< (VMD) 5 % autopsf -nucleic atom
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: false osel: protein or nucleic nfrag: true
Need to have at least one atom in your selection!
>Main< (VMD) 6 % autopsf -protein n2
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
Need to have at least one atom in your selection!
>Main< (VMD) 7 % autopsf -noguess
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
ERROR: psf checking did not work correctly.
There may be something wrong with the input structure.
2
>Main< (VMD) 8 % autopsf -noguess popc128a.pdb
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
ERROR: psf checking did not work correctly.
There may be something wrong with the input structure.
2
>Main< (VMD) 9 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
ERROR: psf checking did not work correctly.
There may be something wrong with the input structure.
2
>Main< (VMD) 10 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads\popc128a.pdb
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
ERROR: psf checking did not work correctly.
There may be something wrong with the input structure.
2
>Main< (VMD) 11 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads\popc128a.pdb
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
Reading PDB CONECT records...
Warning: I couldn't find the original pdb to assign connectivity
Using autogenerated connectivity only
ERROR: psf checking did not work correctly.
There may be something wrong with the input structure.
2
>Main< (VMD) 12 % connect
invalid command name "connect"
invalid command name "connect"
>Main< (VMD) 13 % -molid $molid
can't read "molid": no such variable
>Main< (VMD) 14 % $molid
can't read "molid": no such variable
>Main< (VMD) 15 % pbcwrap $molid
can't read "molid": no such variable
>Main< (VMD) 16 % pbcwrap -molid $molid
can't read "molid": no such variable
>Main< (VMD) 17 % pbcwrap $molid
can't read "molid": no such variable
>Main< (VMD) 18 % autopsf -protein N
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
Need to have at least one atom in your selection!
>Main< (VMD) 19 % autopsf -protein Ni
Welcome to AUTOPSF!
The automatic structure builder.
WORKING ON: top
pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
Need to have at least one atom in your selection!
>Main< (VMD) 20 %