From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 27 2007 - 10:45:00 CDT

Hi Lucie,
the reason you're getting those extra protons is that the default
patching in most of the topology files you'll run across is NTER, so the
NTER patch is applied unless you say otherwise. So in your initial
segment generation, what you ought to do instead is
segment CYP {
    pdb cyp3a4_noheme_nopatch.pdb
    first ACE
    last CT2
}

to avoid getting the autopatches in place of the ones you want.

Peter

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
>
>