From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 06 2014 - 09:59:23 CST

Freda,
  We are finalizing a few last bits of code, then we will be beginning
to make beta versions of VMD 1.9.2 available, and when sufficiently
consistently positive user feedback has been heard for each target
platform, we will make the final release. It's likely a matter of
several weeks now, though I have some travel in the middle of that time
that will slow things a bit.

Cheers,
  John

On Thu, Feb 06, 2014 at 06:25:14PM +0800, Freda Lim (IHPC) wrote:
> Hi Kirby,
>
> Thanks very much!!!
>
> It works! :) (but the results don't quite match what I made manually though. I have to figure out how to make the .cgc works best for me.)
>
> When will the v.1.9.2 VMD be officially release?
>
> freda
>
> -----Original Message-----
> From: Kirby Vandivort [mailto:kvandivo_at_ks.uiuc.edu]
> Sent: Thursday, 6 February, 2014 7:19 AM
> To: Freda Lim (IHPC)
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: How do you construct a .cgc file that actually works?
>
> Using the latest version of VMD that we have here (an alpha of 1.9.2) I loaded the PDB file you attached, browsed and added the user defined cgc file you attached, and it was able to build the residue based coarse grain model for me.
>
> From the error message you are getting, it looks like you are hitting a bug that I fixed last April, so if you get the latest alpha versions of VMD you should be able to try it again and do OK.
>
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Please let us know if you continue to have difficulties after that.
>
> Kirby
>
>
> On 02/05/2014 12:12 AM, Freda Lim (IHPC) wrote:
> > Hi,
> >
> > I have looked up on the format of the .cgc files and have looked at
> > the example .cgc files that comes with VMD.
> >
> > I tried to use the CG builder modelling extension but failed because
> > of the following error. Would someone advise what could have gone
> > wrong? And how could I construct a .cgc file that actually works?
> >
> > Thank you.
> >
> > *Error Log:*
> >
> > atomselect: cannot parse selection text: occupancy >= 0 and segid and
> > ( index 0 or { name H11 and resid 1 and resname HEG } or { name C2 and
> > resid 1 and resname HEG } or { name H21 and resid 1 and resname HEG }
> > or { name H22 and resid 1 and resname HEG } or { name C3 and resid 1
> > and resname HEG } or { name H31 and resid
> > 1 and resname HEG } or { name H32 and resid 1 and resname HEG } )
> >
> > atomselect: cannot parse selection text: occupancy >= 0 and segid and
> > ( index 0 or { name H11 and resid 1 and resname HEG } or { name C2 and
> > resid 1 and resname HEG } or { name H21 and resid 1 and resname HEG }
> > or { name H22 and resid 1 and resname HEG } or { name C3 and resid 1
> > and resname HEG } or { name H31 and resid
> > 1 and resname HEG } or { name H32 and resid 1 and resname HEG } )
> >
> > 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)
> >
> > *Input pdb:*
> >
> > TITLE Gromacs Runs One Microsecond At Cannonball Speeds
> >
> > REMARK THIS IS A SIMULATION BOX
> >
> > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
> >
> > MODEL 1
> >
> > ATOM 1 O1 HEG 1 21.650 29.320 25.900 1.00 0.00
> >
> > ATOM 2 H11 HEG 1 21.710 30.050 26.500 1.00 0.00
> >
> > ATOM 3 C2 HEG 1 22.960 28.820 25.630 1.00 0.00
> >
> > ATOM 4 H21 HEG 1 23.620 29.120 26.430 1.00 0.00
> >
> > ATOM 5 H22 HEG 1 23.330 29.280 24.710 1.00 0.00
> >
> > ATOM 6 C3 HEG 1 22.950 27.270 25.490 1.00 0.00
> >
> > ATOM 7 H31 HEG 1 22.550 26.840 26.410 1.00 0.00
> >
> > ATOM 8 H32 HEG 1 22.270 26.990 24.680 1.00 0.00
> >
> > ATOM 9 O1 EG 2 24.260 26.720 25.240 1.00 0.00
> >
> > ATOM 10 C2 EG 2 24.290 25.290 25.110 1.00 0.00
> >
> > ATOM 11 H21 EG 2 23.630 24.990 24.300 1.00 0.00
> >
> > ATOM 12 H22 EG 2 23.900 24.840 26.030 1.00 0.00
> >
> > ATOM 13 C3 EG 2 25.720 24.730 24.840 1.00 0.00
> >
> > ATOM 14 H31 EG 2 26.110 25.170 23.920 1.00 0.00
> >
> > ATOM 15 H32 EG 2 26.380 25.030 25.650 1.00 0.00
> >
> > ATOM 16 O1 EGO 3 25.750 23.290 24.720 1.00 0.00
> >
> > ATOM 17 C2 EGO 3 27.060 22.740 24.470 1.00 0.00
> >
> > ATOM 18 H21 EGO 3 27.730 23.030 25.280 1.00 0.00
> >
> > ATOM 19 H22 EGO 3 27.460 23.170 23.550 1.00 0.00
> >
> > ATOM 20 C3 EGO 3 27.050 21.190 24.340 1.00 0.00
> >
> > ATOM 21 H31 EGO 3 26.660 20.740 25.250 1.00 0.00
> >
> > ATOM 22 H32 EGO 3 26.390 20.880 23.530 1.00 0.00
> >
> > ATOM 23 O4 EGO 3 28.350 20.670 24.090 1.00 0.00
> >
> > ATOM 24 H41 EGO 3 28.310 19.730 24.020 1.00 0.00
> >
> > TER
> >
> > ENDMDL
> >
> > *.cgc file:*
> >
> > CGBEGIN
> >
> > HEG HEG2 0
> >
> > HEG O1 0
> >
> > HEG H11 0
> >
> > HEG C2 0
> >
> > HEG H21 0
> >
> > HEG H22 0
> >
> > HEG C3 0
> >
> > HEG H31 0
> >
> > HEG H32 0
> >
> > CGEND
> >
> > CGBEGIN
> >
> > EG EG2 0
> >
> > EG O1 0
> >
> > EG C2 0
> >
> > EG H21 0
> >
> > EG H22 0
> >
> > EG C3 0
> >
> > EG H31 0
> >
> > EG H32 0
> >
> > CGEND
> >
> > CGBEGIN
> >
> > EGO EGO2 0
> >
> > EGO O1 0
> >
> > EGO C2 0
> >
> > EGO H21 0
> >
> > EGO H22 0
> >
> > EGO C3 0
> >
> > EGO H31 0
> >
> > EGO H32 0
> >
> > EGO O4 0
> >
> > EGO H41 0
> >
> > CGEND
> >
> > *Freda LIM, PhD :: Scientist II:: Consumer Care Team :: Department of
> > Materials Science and Engineering :: Institute of High Performance
> > Computing :: Agency for Science, Technology and Research (A*STAR)*
> >
> > 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632 :: DID: (65) 6419 1224 ::
> > limch_at_ihpc.a-star.edu.sg <mailto:limch_at_ihpc.a-star.edu.sg>
> >
> >
> > IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This
> > email is confidential and may be privileged. If you are not the
> > intended recipient, please delete it and notify us immediately. Please
> > do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.
>
>
> --
>
> Kirby Vandivort Theoretical and
> Senior Research Programmer Computational Biophysics
> Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
> http://www.ks.uiuc.edu/~kvandivo/ University of Illinois
> Phone: (217) 244-5711 405 N. Mathews Ave
> Fax : (217) 244-6078 Urbana, IL 61801, USA
>
> IHPC Values :: Impact :: Honesty :: Performance :: Co-operation
> This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you.

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/