From: Stamatia Zavitsanou (zavitsanoustamatia_at_gmail.com)
Date: Tue Jul 17 2018 - 08:56:10 CDT

Dear Peter,

Thank you for answering,

Here is the error that autopsf gives when I try to "Create the chains"
having loaded "toppar_water_ions_namd.str", "top_all36_cgenff.rtf" and the
hybrid.rtf file I have created.

ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
    while executing
"segment $segid {
      pdb $segfile

      # We alias the C-terminal OXT atoms to OT2 so that psfgen has to
guess one atom less.
      # Otherwise psf..."
    (procedure "psfsegments" line 37)
    invoked from within
"psfsegments $logfileout"
    (procedure "::autopsf::afterchains_gui" line 66)
    invoked from within
"::autopsf::afterchains_gui"
    invoked from within
".autopsf.chains.finish invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .autopsf.chains.finish"
    (command bound to event)

When I do it with -dispdev text -e psfgen (where psfgen is the text below)

mol delete all
mol load pdb /home/matina/Desktop/CGenff/complex007.pdb
set chainA [atomselect top "chain A and not hydrogen"]
set chainB [atomselect top "chain B and not hydrogen"]
set chainX [atomselect top "residuetype nothing"]
$chainA writepdb chainA.pdb
$chainB writepdb chainB.pdb
$chainX writepdb chainX.pdb
package require psfgen
topology /home/matina/Desktop/CGenff/top_all36_cgenff.rtf
topology /home/matina/Desktop/CGenff/toppar_water_ions_namd.str
topology /home/matina/Desktop/CGenff/hybrid007.rtf
pdbalias HIS HSD
pdbalias atom SER HG HG1
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {
  first NONE
  last NONE
  pdb chainA.pdb
}

segment B {
  first NONE
  last NONE
  pdb chainB.pdb
}

segment X {
  first NONE
  last NONE
  pdb chainX.pdb
}

coordpdb chainA.pdb A
coordpdb chainB.pdb B
coordpdb chainX.pdb X

guesscoord
writepdb psf-complex.pdb
writepsf psf-complex.psf
exit

I get this

 reading topology file /home/matina/Desktop/CGenff/hybrid007.rtf

psfgen) ERROR! FAILED TO RECOGNIZE ´╗┐ATOM. Line 1: ´╗┐ATOM CAQ C1AQ -0.161

psfgen) no residue in progress for atom
psfgen) ERROR! Failed to parse atom statement. Line 2: ATOM CAP C1AP
-0.055

psfgen) no residue in progress for atom
psfgen) ERROR! Failed to parse atom statement. Line 3: ATOM NAO N1AO
-0.522

psfgen) no residue in progress for atom
psfgen) ERROR! Failed to parse atom statement. Line 4: ATOM CAN C1AN
0.237
........

psfgen) no residue in progress for bond
psfgen) ERROR! Failed to parse bond statement. Line 44: BOND CAQ H11

psfgen) no residue in progress for bond
psfgen) ERROR! Failed to parse bond statement. Line 45: BOND CAQ H12

psfgen) no residue in progress for bond
psfgen) ERROR! Failed to parse bond statement. Line 46: BOND CAQ H13

psfgen) no residue in progress for bond
psfgen) ERROR! Failed to parse bond statement. Line 47: BOND CAQ CAP
...............

psfgen) aliasing residue SER atom HG to HG1
psfgen) aliasing residue HIS to HSE
psfgen) aliasing residue ILE atom CD1 to CD
psfgen) building segment A
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE
psfgen) reading residues from pdb file chainA.pdb
psfgen) unknown residue type MET
psfgen) unknown residue type ALA
psfgen) unknown residue type GLY
psfgen) unknown residue type ARG
psfgen) unknown residue type LEU
psfgen) unknown residue type PRO
....................
psfgen) extracted 418 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type MET
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
Info) VMD for LINUXAMD64, version 1.9.4a12 (December 21, 2017)
Info) Exiting normally.

Thank you again,
Matina

On 17 July 2018 at 16:00, Peter Freddolino <petefred_at_umich.edu> wrote:

> Dear Matina,
> It would be helpful to paste the error output that you get from VMD when
> you try to run this. Chances are it is having trouble with your topology
> file, but without more information it is impossible to guess what is going
> on.
> Thanks,
> Peter
>
>
> On Tue, Jul 17, 2018 at 4:59 AM, Stamatia Zavitsanou <
> zavitsanoustamatia_at_gmail.com> wrote:
>
>> Hello,
>> I am trying to generate a PSF file in order to run a NAMD/FEP simulation--000000000000fd16b70571324eda--