From: Dong Luo (us917_at_yahoo.com)
Date: Tue Apr 02 2013 - 11:29:46 CDT

Hi Chaofu, I run into the same problem when directly converting a pdb file downloaded online. The reason is that CG Tools plugin require VMD friendly pdb file. If a psf file is presented, the coupled pdb file is normally prepared by VMD too. I tested that such a friendly pdb file can be converted without psf file. To reprepare a pdb file into psf/pdb pairs by VMD, please check the user guide/tutorials of psfgen or NAMD, which includes step by step instruction how to do so. Sorry that I did not check it before previous reply. Dong ________________________________ From: WuChaofu <xiaowu759_at_hotmail.com> To: Dong Luo <us917_at_yahoo.com> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu> Sent: Monday, April 1, 2013 6:52 PM Subject: RE: vmd-l: CGTools with pdb and top files 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 } ) ________________________________ 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