VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 17 2018 - 09:37:37 CDT

Could you post your hybrid.rtf file? It is clearly not liking something
there. Based on the error output I am guessing that you are missing the
RESI line.
Best,
Peter

On Tue, Jul 17, 2018 at 9:56 AM, Stamatia Zavitsanou <
zavitsanoustamatia_at_gmail.com> wrote:

> 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.
>>> I use input from CGenFF.
>>> I have created the dual topology file (hybrid.rtf which is created after
>>> I have merged the reference with the mutant ligand into one file) and the
>>> complex.pdb file of the protein and the two ligands.
>>> I want to use autopsf and I load the complex.pdb file, the topology of
>>> the two ligands, hybrid.rtf file and these two files that I have found from
>>> CGenFF, toppar_water_ions_namd.str, top_all36_cgenff.rtf. Is this correct?
>>> It only creates a complex007_autopsf-temp.pdb not a final I think it's
>>> because VMD cannot read my hybrid.rtf file. Has anyone tried to do anything
>>> like that?
>>>
>>> If not how do you create the PSF file to run a NAMD/FEP simulation?
>>>
>>> Thank you,
>>> Matina
>>>
>>
>>
>