VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Mar 16 2016 - 09:23:48 CDT

Hi Stefan,
Digging a bit deeper here — it looks like the different behavior is because your original no-hydrogen pdb file specifies the elements for each atom explicitly, whereas this is lost in the hydrogen-added file. If you add the element field back into the hydrogen-added file, it works fine. Otherwise, VMD doesn’t know what element to guess that “SD” is, so it assigns it a lower vdw radius than is appropriate for sulfur, and misses that bond.
Best,
Peter

> On Mar 16, 2016, at 10:01 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
>
> Hello Peter, the structure comes from the 1m6b OPM http://opm.phar.umich.edu/protein.php?pdbid=1m6b but I assume the original PDB structure would have the same issue.
>
> The bond is long but for some reason without the hydrogens it gets bonded. I moved the atom closer and the bond then gets fixed.
> So it is a combination of distance plus some other unknown factor involving the hydrogens. I was wondering what that factor could be.
>
> It actually happens in various proteins that I've tested, so it's definitely not a unique exception that could be ignored.
>
> On Wed, Mar 16, 2016 at 2:55 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> Hi Stefan,
> The SD-CE bond in your structure is quite long — where did this structure come from? I do not know why the bond guessing is working differently with/without hydrogens, but probably the long bond there is a big part of the problem.
> Best,
> Peter
>
> > On Mar 16, 2016, at 7:25 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
> >
> > As the title says. I protonated the residue and suddenly the CE carbon is detached from the residue and the "protein" atomselection fails for that atom.
> > Do you have any ideas what causes this? It seems to me like a problem in VMD automatic bond guessing. `mol bondsrecalc molid` doesn't help either.
> >
> > File1.pdb
> >
> > ATOM 1 N MET B300 1.059 -7.535 62.937 1.00 16.59 B N
> > ATOM 2 CA MET B300 0.373 -6.852 61.829 1.00 17.27 B C
> > ATOM 3 C MET B300 -0.113 -5.426 62.105 1.00 17.06 B C
> > ATOM 4 O MET B300 -0.091 -4.976 63.233 1.00 17.04 B O
> > ATOM 5 CB MET B300 -0.785 -7.700 61.331 1.00 17.64 B C
> > ATOM 6 CG MET B300 -1.825 -8.046 62.383 1.00 20.84 B C
> > ATOM 7 SD MET B300 -3.507 -7.963 61.711 1.00 28.56 B S
> > ATOM 8 CE MET B300 -3.276 -8.786 59.820 1.00 24.84 B C
> >
> > File2.pdb
> >
> > ATOM 1 N MET B300 1.059 -7.535 62.937 0.00 0.00 B
> > ATOM 2 CA MET B300 0.373 -6.852 61.829 0.00 0.00 B
> > ATOM 3 C MET B300 -0.113 -5.426 62.105 0.00 0.00 B
> > ATOM 4 O MET B300 -0.091 -4.976 63.233 0.00 0.00 B
> > ATOM 5 CB MET B300 -0.785 -7.700 61.331 0.00 0.00 B
> > ATOM 6 CG MET B300 -1.825 -8.046 62.383 0.00 0.00 B
> > ATOM 7 SD MET B300 -3.507 -7.963 61.711 0.00 0.00 B
> > ATOM 8 CE MET B300 -3.276 -8.786 59.820 0.00 0.00 B
> > ATOM 9 HE1 MET B300 -3.248 -9.727 60.020 0.00 0.00 B
> > ATOM 10 HB2 MET B300 -1.251 -7.212 60.574 0.00 0.00 B
> > ATOM 11 H MET B300 0.841 -7.371 63.930 0.00 0.00 B
> > ATOM 12 HG3 MET B300 -1.723 -7.406 63.170 0.00 0.00 B
> > ATOM 13 HG2 MET B300 -1.630 -8.980 62.744 0.00 0.00 B
> > ATOM 14 HE3 MET B300 -4.069 -8.472 59.374 0.00 0.00 B
> > ATOM 15 HE2 MET B300 -2.446 -8.390 59.536 0.00 0.00 B
> > ATOM 16 HB3 MET B300 -0.420 -8.567 60.950 0.00 0.00 B
> > ATOM 17 HA MET B300 1.028 -6.810 61.040 0.00 0.00 B
>
>