[gmx-users] Secondary structure not visible afterconverting from .gro to .pdb
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu May 29 21:26:11 CEST 2014
Hey,
The .gro file format has no information about chains, so it won't write any
when converting to PDB, and Pymol gets mixed up, stopping after the first
chain. A solution is to use trjconv and a tpr file to convert the .gro file
to .pdb. The chains will then be set according to the molecules defined in
the .tpr.
Cheers,
Tsjerk
On Thu, May 29, 2014 at 11:33 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
> wrote:
> Hi,
>
> Gromacs sometimes omits chain labels when writing PDBs, so there might
> actually be something to fix. I don't remember under exactly what
> circumstances though, and the reason could be perfectly reasonable.
>
> Furthermore, in pymol you can assign the secondary structure to a protein
> in case pymol doesn't do so automatically, which happens e.g. for
> multi-MODEL structures.
>
> Kind regards,
> Erik
>
> On 29 May 2014, at 07:16, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > It seems like you've generated a structure that does not match the
> > preconceptions of PyMol. What is there to solve?
> >
> > Mark
> > On May 29, 2014 8:09 AM, "bharat gupta" <bharat.85.monu at gmail.com>
> wrote:
> >
> >> Sorry, it was my mistake actually i opened this file in excel that's
> why I
> >> got that kind of numbering.
> >>
> >> But still, whats the solution to my problem. I will post this query in
> >> Pymol mailing list also.
> >>
> >>
> >> On Thu, May 29, 2014 at 2:56 PM, Mark Abraham <mark.j.abraham at gmail.com
> >>> wrote:
> >>
> >>> Hi,
> >>>
> >>> That seems like a bug. What GROMACS command and version produced it?
> >>>
> >>> Mark
> >>> On May 29, 2014 6:40 AM, "bharat gupta" <bharat.85.monu at gmail.com>
> >> wrote:
> >>>
> >>>> Thanks you all for your responses. As far the chain name is concerned,
> >>> that
> >>>> can be worked out by a simple script. But I found another issue in the
> >>>> converted pdb file that gromacs gives some weird numbering after atom
> >>>> 99999. Here's the sample from the converted pdb file :-
> >>>>
> >>>> ATOM 99999 HA ALA X 609 145.370 109.310 33.980 0.00 0.00
> >>>>
> >>>> ATOM 186a0 CB ALA X 609 144.460 108.520 35.770 0.00 0.00
> >>>>
> >>>> ATOM 186a1 HB1 ALA X 609 143.430 108.800 35.570 0.00 0.00
> >>>>
> >>>> ATOM 186a2 HB2 ALA X 609 144.600 107.490 35.440 0.00 0.00
> >>>>
> >>>> ATOM 186a3 HB3 ALA X 609 144.590 108.530 36.850 0.00 0.00
> >>>>
> >>>> ATOM 186a4 C ALA X 609 145.090 110.890 35.400 0.00 0.00
> >>>>
> >>>> ATOM 186a5 O ALA X 609 144.400 111.540 34.620 0.00 0.00
> >>>>
> >>>> ATOM 186a6 N PHE X 610 145.520 111.380 36.560 0.00 0.00
> >>>>
> >>>> ATOM 186a7 H PHE X 610 146.110 110.800 37.130 0.00 0.00
> >>>>
> >>>> ATOM 186a8 CA PHE X 610 145.120 112.700 37.050 0.00 0.00
> >>>>
> >>>> ATOM 186a9 HA PHE X 610 144.160 113.010 36.630 0.00 0.00
> >>>>
> >>>> ATOM 186aa CB PHE X 610 145.000 112.640 38.580 0.00 0.00
> >>>>
> >>>> ATOM 186ab HB1 PHE X 610 145.860 112.140 39.030 0.00 0.00
> >>>>
> >>>> ATOM 186ac HB2 PHE X 610 145.010 113.650 38.970 0.00 0.00
> >>>>
> >>>> ATOM 186ad CG PHE X 610 143.710 112.010 39.090 0.00 0.00
> >>>>
> >>>> ATOM 186ae CD1 PHE X 610 142.590 112.820 39.360 0.00 0.00
> >>>>
> >>>> ATOM 186af HD1 PHE X 610 142.620 113.880 39.170 0.00 0.00
> >>>>
> >>>> ATOM 186b0 CD2 PHE X 610 143.630 110.610 39.300 0.00 0.00
> >>>>
> >>>> ATOM 186b1 HD2 PHE X 610 144.480 109.980 39.090 0.00 0.00
> >>>>
> >>>> ATOM 186b2 CE1 PHE X 610 141.400 112.240 39.840 0.00 0.00
> >>>>
> >>>> ATOM 186b3 HE1 PHE X 610 140.540 112.860 40.040 0.00 0.00
> >>>>
> >>>> ATOM 186b4 CE2 PHE X 610 142.440 110.040 39.780 0.00 0.00
> >>>>
> >>>> ATOM 186b5 HE2 PHE X 610 142.380 108.970 39.940 0.00 0.00
> >>>>
> >>>> ATOM 186b6 CZ PHE X 610 141.330 110.860 40.060 0.00 0.00
> >>>>
> >>>> ATOM 186b7 HZ PHE X 610 140.410 110.430 40.430 0.00 0.00
> >>>>
> >>>> ATOM 186b8 C PHE X 610 146.160 113.780 36.700 0.00 0.00
> >>>>
> >>>> ATOM 186b9 O PHE X 610 145.840 114.970 36.770 0.00 0.00
> >>>>
> >>>> ATOM 186ba N GLU X 611 147.400 113.400 36.350 0.00 0.00
> >>>>
> >>>> ATOM 186bb H GLU X 611 147.610 112.410 36.340 0.00 0.00
> >>>>
> >>>> ATOM 186bc CA GLU X 611 148.490 114.340 36.120 0.00 0.00
> >>>>
> >>>> ATOM 186bd HA GLU X 611 148.460 115.100 36.900 0.00 0.00
> >>>>
> >>>> ATOM 186be CB GLU X 611 149.840 113.580 36.110 0.00 0.00
> >>>>
> >>>> ATOM 186bf HB1 GLU X 611 149.720 112.590 35.680 0.00 0.00
> >>>>
> >>>> ATOM 186c0 HB2 GLU X 611 150.560 114.090 35.470 0.00 0.00
> >>>>
> >>>> ATOM 186c1 CG GLU X 611 150.480 113.460 37.510 0.00 0.00
> >>>>
> >>>> ATOM 186c2 HG1 GLU X 611 149.840 112.900 38.170 0.00 0.00
> >>>>
> >>>> ATOM 186c3 HG2 GLU X 611 151.410 112.910 37.430 0.00 0.00
> >>>>
> >>>> ATOM 186c4 CD GLU X 611 150.780 114.810 38.130 0.00 0.00
> >>>>
> >>>> ATOM 186c5 OE1 GLU X 611 150.020 115.240 39.030 0.00 0.00
> >>>>
> >>>> ATOM 186c6 OE2 GLU X 611 151.720 115.490 37.650 0.00 0.00
> >>>>
> >>>> ATOM 186c7 C GLU X 611 148.340 115.110 34.790 0.00 0.00
> >>>>
> >>>> ATOM 186c8 O GLU X 611 148.850 116.220 34.680 0.00 0.00
> >>>>
> >>>> ATOM 186c9 N VAL X 612 147.610 114.560 33.820 0.00 0.00
> >>>>
> >>>>
> >>>> On Thu, May 29, 2014 at 12:58 PM, Christopher Neale <
> >>>> chris.neale at alum.utoronto.ca> wrote:
> >>>>
> >>>>> [image: Boxbe] <https://www.boxbe.com/overview> This message is
> >>>> eligible
> >>>>> for Automatic Cleanup! (chris.neale at alum.utoronto.ca) Add cleanup
> >>> rule<
> >>>>
> >>>
> >>
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> >>>> More
> >>>>> info<
> >>>>
> >>>
> >>
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> >>>>>
> >>>>>
> >>>>> Sounds reasonable now. If 10 molecules are all listed as part of the
> >>> same
> >>>>> chain (PDB format) then maybe Pymol will stop rendering after the
> >> first
> >>>>> "chain". So either script changing the chain info or find some other
> >>> way
> >>>> to
> >>>>> have them listed as different chains in the .pdb or (perhaps) just
> >> use
> >>> a
> >>>>> .gro -- if pymol will work with this -- since AFAIK a .gro file does
> >>> not
> >>>>> list chains so Pymol may be forced to figure things out on its own.
> >>>>>
> >>>>> At this point, it does really seem like a Pymol issue, so I agree
> >> with
> >>>>> previous posters that you will get the most useful help on a Pymol
> >>>> mailing
> >>>>> list.
> >>>>>
> >>>>> Chris.
> >>>>> ________________________________________
> >>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> >>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> >> bharat
> >>>>> gupta <bharat.85.monu at gmail.com>
> >>>>> Sent: 28 May 2014 21:24
> >>>>> To: Discussion list for GROMACS users
> >>>>> Subject: Re: [gmx-users] Secondary structure not visible after
> >>> converting
> >>>>> from .gro to .pdb
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> I energy minimized a protein consisting 10 chains using gromacs.
> >> When I
> >>>>> converted the structure of the protein from gro format to pdb format
> >> to
> >>>>> visualize in Pymol, it shows only one chain in ribbon form and rest
> >> of
> >>>> the
> >>>>> chains are not shown ... How to rectify this error ??
> >>>>>
> >>>>>
> >>>>> Regards
> >>>>> -----
> >>>>> Bharat
> >>>>> --
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--
Tsjerk A. Wassenaar, Ph.D.
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