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

bharat gupta bharat.85.monu at gmail.com
Thu May 29 06:38:05 CEST 2014


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
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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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