VMD-L Mailing List

From: WuChaofu (xiaowu759_at_hotmail.com)
Date: Mon Apr 01 2013 - 23:59:51 CDT

Dear Dong and VMDers,
Thank you very much! I had thought so, but an error arises as presented below. Thus, this might be due to that psf file is not provided. How to deal with this problem?
Chaofu Wu

No PSF file loaded. I'll go ahead and do the coarse graining, but it might not work properly. You might want to run again after loading a PSF file.
Apply bead with bead 228
ERROR>syntax error
more detail is as follows:
atomselect: cannot parse selection text:  occupancy >= 0 and segid  and ( index 1 or { name H11 and resid 1 and resname  tMA } or { name H12 and resid 1 and resname  tMA } or { name C2 and resid 1 and resname  tMA } or { name C6 and resid 1 and resname  tMA } or { name H61 and resid 1 and resname  tMA } or { name H62 and resid 1 and resname  tMA } or { name H63 and resid 1 and resname  tMA } or { name C3 and resid 1 and resname  tMA } or { name O31 and resid 1 and resname  tMA } or { name O4 and resid 1 and resname  tMA } or { name C5 and resid 1 and resname  tMA } or { name H51 and resid 1 and resname  tMA } or { name H52 and resid 1 and resname  tMA } or { name H53 and resid 1 and resname  tMA } )
atomselect: cannot parse selection text:  occupancy >= 0 and segid  and ( index 1 or { name H11 and resid 1 and resname  tMA } or { name H12 and resid 1 and resname  tMA } or { name C2 and resid 1 and resname  tMA } or { name C6 and resid 1 and resname  tMA } or { name H61 and resid 1 and resname  tMA } or { name H62 and resid 1 and resname  tMA } or { name H63 and resid 1 and resname  tMA } or { name C3 and resid 1 and resname  tMA } or { name O31 and resid 1 and resname  tMA } or { name O4 and resid 1 and resname  tMA } or { name C5 and resid 1 and resname  tMA } or { name H51 and resid 1 and resname  tMA } or { name H52 and resid 1 and resname  tMA } or { name H53 and resid 1 and resname  tMA } )
    while executing
"atomselect $molid "$fullbeadsel""
    (procedure "apply_bead" line 66)
    invoked from within
"apply_bead $cgbead $molid $rcgout"
    (procedure "::cgtools::apply_database" line 26)
    invoked from within
"::cgtools::apply_database $::cggui::currentToCGMol  $::cggui::toCGoutpdbfile  $::cggui::revcgfile"
    (procedure "::cggui::buildResidueCGExecute" line 43)
    invoked from within
"::cggui::buildResidueCGExecute"
    invoked from within
".cggui.toCGResidueFrame.applyDB invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .cggui.toCGResidueFrame.applyDB"
    (command bound to event)
________________________________
> Date: Mon, 1 Apr 2013 08:39:56 -0700
> From: us917_at_yahoo.com
> Subject: Re: vmd-l: CGTools with pdb and top files
> To: xiaowu759_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> By information on http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/,
> I don't see why psf file is required for the AA (all-atoms) model. Only
> pdb file is used for the conversion. No Charmm or OPLS force field
> parameter files are needed. But you do need a psf file to run
> simulations for newly coverted CG molecule. Just follow instructions in
> the link.
>
> Dong
>
> ________________________________
> From: WuChaofu <xiaowu759_at_hotmail.com>
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Sent: Monday, April 1, 2013 3:55 AM
> Subject: vmd-l: CGTools with pdb and top files
>
> Dear VMDers,
> I try to use the CGTools plugin to perform the conversion from AA to
> CG. As confirmed that, both pdb and psf files are required for the AA
> model. However, I have only a top file in the format of GROMACS instead
> of a psf file. In the top file, all parameters are described by the
> OPLSAA force field. How should I perform the conversion with only pdb
> and top file in hand? Or How should I modify the tool to achieve this?
> Please give me some hints. Thank you very much!
> Chaofu Wu
>
>