VMD-L Mailing List

From: lucie huynh (luciehuynh_at_gmail.com)
Date: Thu Mar 29 2007 - 03:24:01 CDT

Hi,
Peter Freddolino helped me to solve my psf creating problem: I didn't pay
attention to the break line when I entered the commands:
segment CYP {
   pdb cyp3a4_noheme_nopatch.pdb
   first ACE
   last CT2
}

Now it's ok, I built my psf file with psfgen and my water box with the
solvate package!
Thank you again for your help and your attention!
Have a nice day!

Lucie

2007/3/29, John Stone <johns_at_ks.uiuc.edu>:
>
>
> 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
>