[gmx-users] Secondary structure not visible afterconverting from .gro to .pdb

Mark Abraham mark.j.abraham at gmail.com
Thu May 29 08:17:04 CEST 2014 

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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-request at gromacs.org.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list