VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 28 2007 - 22:27:50 CDT

Hi,
  Can you send me the PDB file you generated so I can have a look?
When you say it can't be loaded, is that into VMD, or into psfgen, or both?
You can help us to help you more efficiently by providing the text of
any error messages you receive when you're having problems, as they typically
indicate the precise issue you're having. It saves a lot of back and forth
over email if you can provide as much detail up-front as possible.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 28, 2007 at 10:59:47AM +0200, lucie huynh wrote:
> Hi,
> Thanks for your reply.
> I loaded my .psf file (from CHARMM 26) with VMD, I saved it in .pdb but it
> can't be loaded in VMD.
> Does the problem come from the psf file had not be converted into a pdb file
> but had just been saved in .pdb?
> Thanks again for your help.
> Have a nice day!
>
> Lucie
>
>
> 2007/3/27, John Stone <johns_at_ks.uiuc.edu>:
> >
> >Hi,
> > Is your existing CHARMM PSF file an EXT, CMAP, or CHEQ variant?
> >Although VMD itself already reads all of the new CHARMM PSF formats just
> >fine,
> >psfgen is still in the process of being updated. The PSF reader in psfgen
> >is somewhat more complex since it must read and use all of the fields in
> >a PSF file unlike VMD which can safely ignore many of the entries it
> >doesn't need.
> >
> >One workaround for this problem in the short term would be to
> >use VMD to read in your existing PSF file, and then save it out again
> >as a PDB. From there, you should be able to load the PDB file and run
> >psfgen or the AutoPSF plugin to create a new PSF file without the issue
> >that you're running into now. All of this is assuming that the cause of
> >your problem is one of the new versions of the PSF format that psfgen
> >doesn't yet fully understand. Let us know if that works for you.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Mar 27, 2007 at 04:54:08PM +0200, lucie huynh wrote:
> >> Hi everybody,
> >>
> >> I'd like to build a water box for a protein. I have already a psf file
> >that
> >> I buid from Charmm but it seems that VMD could'nt read it.
> >> >package require solvate
> >> 1.2
> >> >solvate cyp4.psf cyp4.pdb -t 10 -o cyp5_wb
> >> reading structure from psf file cyp4.psf
> >> error reading atoms
> >> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >>
> >> So I'm trying to generate a psf file of my protein with ACE patch at
> >N-term
> >> and CT2 patch at C-term.
> >> Here are what I entered in Tk console and his messages:
> >>
> >> >package require psfgen
> >> >topology top_all22_prot2.inp
> >> >pdbalias residue HIS HSD
> >> >pdbalias atom ILE CD1 CD
> >> >pdbalias atom HSD H HN
> >> >pdbalias atom HIS H HN
> >>
> >> >segment CYP {pdb cyp3a4_noheme_nopatch.pdb}
> >> building segment CYP
> >> reading residues from pdb file cyp3a4_noheme_nopatch.pdb
> >> extracted 470 residues from pdb file
> >> Info: generating structure...
> >> Info: skipping improper N-C-CA-HN at beginning of segment.
> >> Info: skipping conformation C-N-CA-C at beginning of segment.
> >> Info: skipping conformation C-CA-N-HN at beginning of segment.
> >> Info: skipping bond C-N at end of segment.
> >> Info: skipping improper C-CA-N-O at end of segment.
> >> Info: skipping conformation CA-C-N-CA at end of segment.
> >> Info: skipping conformation N-CA-C-O at end of segment.
> >> Info: skipping conformation N-CA-C-N at end of segment.
> >> Info: segment complete.
> >>
> >> >patch ACE CYP:28
> >> applying patch ACE to 1 residues
> >> no atom HN in residue HSD:28 of segment CYP
> >> Warning: add improper failed in patch ACE
> >> no atom HN in residue HSD:28 of segment CYP
> >> Warning: add conformation failed in patch ACE
> >>
> >> >patch CT2 CYP:499
> >> applying patch CT2 to 1 residues
> >>
> >>
> >> It seems there's a problem in the recognition of the atom HN of the
> >HSD:28
> >> which is the first residu in my pdb file.
> >> The pdb I obtain through the psfgen has the patch ACE at the N-term but
> >VMD
> >> has also added 3 H to the N-term:
> >>
> >> ATOM 1 CAY HSD 28 -29.922 7.380 -12.479 0.00 0.00
> >> CYP
> >> ATOM 2 HY1 HSD 28 -30.569 8.125 -12.318 0.00 0.00
> >> CYP
> >> ATOM 3 HY2 HSD 28 -29.127 7.483 -11.882 0.00 0.00
> >> CYP
> >> ATOM 4 HY3 HSD 28 -30.365 6.500 -12.308 0.00 0.00
> >> CYP
> >> ATOM 5 CY HSD 28 -29.620 7.412 -13.432 0.00 0.00
> >> CYP
> >> ATOM 6 OY HSD 28 -28.973 6.667 -13.594 0.00 0.00
> > CYP
> >>
> >> ATOM 7 N HSD 28 -30.070 8.178 -13.891 1.00 0.00
> >> CYP
> >> ATOM 8 HT1 HSD 28 -31.062 8.054 -13.868 0.00 0.00
> >> CYP
> >> ATOM 9 HT2 HSD 28 -29.824 9.037 -13.442 0.00 0.00
> >> CYP
> >> ATOM 10 HT3 HSD 28 -29.620 7.412 -13.432 0.00 0.00
> >> CYP
> >> ATOM 11 CA HSD 28 -29.618 8.226 -15.315 1.00 0.00
> >> CYP
> >> ATOM 12 HA HSD 28 -29.861 7.312 -15.856 1.00 0.00
> >> CYP
> >> ATOM 13 ND1 HSD 28 -32.203 7.912 -17.008 1.00 0.00
> >> CYP
> >>
> >> I have the same problem at the C-term: patch CT2, plus OT1, OT2:
> >>
> >> ATOM 7645 C THR 499 -23.671 -60.575 -22.449 1.00 0.00
> >> CYP
> >> ATOM 7646 O THR 499 -22.471 -60.357 -22.741 1.00 0.00
> >> CYP
> >> ATOM 7647 NT THR 499 -24.122 -61.292 -21.917 0.00 0.00
> >> CYP
> >> ATOM 7648 HT1 THR 499 -23.430 -61.930 -21.578 0.00 0.00
> >> CYP
> >> ATOM 7649 HT2 THR 499 -25.107 -61.121 -21.910 0.00 0.00
> >> CYP
> >> ATOM 7650 OT1 THR 499 -22.772 -60.140 -22.504 0.00 0.00
> >> CYP
> >> ATOM 7651 OT2 THR 499 -24.119 -61.425 -22.173 0.00 0.00
> >> CYP
> >> ATOM 7652 N THR 499 -24.109 -58.336 -23.384 1.00 0.00
> >> CYP
> >> ATOM 7653 HN THR 499 -23.578 -58.399 -24.229 0.00 0.00
> > CYP
> >>
> >> I tried to add patch NONE CYP:28/499 before adding patch ACE and CT2,
> >but
> >> the termini are still NH3 and COO.
> >> It seems that VMD systematically add the H3 and the OO.
> >>
> >> Could anyone help me to solve this problem?
> >> Maybe it comes from the error when building the segment CYP:
> >>
> >> >segment CYP {pdb cyp3a4_noheme_nopatch.pdb}
> >> building segment CYP
> >> reading residues from pdb file cyp3a4_noheme_nopatch.pdb
> >> extracted 470 residues from pdb file
> >> Info: generating structure...
> >> Info: skipping improper N-C-CA-HN at beginning of segment.
> >> Info: skipping conformation C-N-CA-C at beginning of segment.
> >> Info: skipping conformation C-CA-N-HN at beginning of segment.
> >> Info: skipping bond C-N at end of segment.
> >> Info: skipping improper C-CA-N-O at end of segment.
> >> Info: skipping conformation CA-C-N-CA at end of segment.
> >> Info: skipping conformation N-CA-C-O at end of segment.
> >> Info: skipping conformation N-CA-C-N at end of segment.
> >> Info: segment complete.
> >>
> >> Thanks a lot for your help or any suggestion that will help!
> >>
> >> Lucie Huynh
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078