[gmx-users] Secondary structure not visible afterconvertingfrom .gro to .pdb
bharat gupta
bharat.85.monu at gmail.com
Fri May 30 02:04:23 CEST 2014
Thank Tserjk... This worked successfully...It was really a great help..
On Fri, May 30, 2014 at 4:26 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
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>
> 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<
> > >>>>
> > >>>
> > >>
> >
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3Doi046bUrsy2jqdu3iPnMMDCfyxQGd9H08PN4xbZvrX0lyY0RwBuRwdHS4pFOIZVoyfPFJ9vyW75%252BwqZhjpzw5%252FrFk%252FHHZGCIRYvQlEX2OF9PVsbhdJ%252FyPf4yFYvE%252BQYXTxDxD4%252FhfEYIeaEBhvYXpg%253D%253D%26key%3DsHoPB0eYxMOHvJ8FW6tF%252BAaRR%252Fe19I313eb4foyp5Sk%253D&tc_serial=17412285738&tc_rand=1480244079&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> > >>>> |
> > >>>> More
> > >>>>> info<
> > >>>>
> > >>>
> > >>
> >
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=17412285738&tc_rand=1480244079&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> > >>>>>
> > >>>>>
> > >>>>> 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.
> --
> Gromacs Users mailing list
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