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

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu May 29 11:33:49 CEST 2014 

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
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>>>> 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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