VMD-L Mailing List

From: lucie huynh (luciehuynh_at_gmail.com)
Date: Wed Mar 28 2007 - 03:59:47 CDT

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
>