VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Mar 16 2016 - 08:55:12 CDT

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