[gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

Justin Lemkul jalemkul at vt.edu
Thu May 29 04:13:19 CEST 2014 


On 5/28/14, 10:04 PM, bharat gupta wrote:
> Here's the details of  my topol.top file:
>
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
> #include "topol_Protein_chain_G.itp"
> #include "topol_Protein_chain_H.itp"
> #include "topol_Protein_chain_I.itp"
> #include "topol_Protein_chain_J.itp"
>
> ; Include water topology
> #include "oplsaa.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "oplsaa.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> Protein_chain_C     1
> Protein_chain_D     1
> Protein_chain_E     1
> Protein_chain_F     1
> Protein_chain_G     1
> Protein_chain_H     1
> Protein_chain_I     1
> Protein_chain_J     1
> SOL         288169
> NA               144
>

Visualization of the structure has nothing to do with how Gromacs organizes or 
interprets a topology.  PyMOL is interpreting the coordinates as you see it.  If 
it is incorrect (which does happen, especially with beta-strands), there are 
commands you can use to alter the representation.

-Justin

>
>
>
> On Thu, May 29, 2014 at 10:53 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>
>> Thanks Chris, I will check it.
>>
>> What I suspect is that it could be due to multiple number of chains in my
>> protein. Do I need to treat this protein in a separate way during pdb2gmx
>> step ??
>>
>>
>> On Thu, May 29, 2014 at 10:42 AM, Christopher Neale <
>> chris.neale at alum.utoronto.ca> wrote:
>>
>>> I sometimes see this in VMD if the coordinates are truly awful (e.g, if
>>> the C-alpha atoms are way too far apart, then VMD does not recognize it as
>>> a proper backbone since no topology information is loaded and connectivity
>>> is inferred from distances). I also see this for some crystal structures
>>> (in VMD) and I am not sure exactly why, but I presume that something is not
>>> falling into an "accepted" region of conformational space to be recognized
>>> as a protein backbone. I presume the same is true for Pymol.
>>>
>>> Try to run a very small amount of MD and see if that improves things. It
>>> always does for me.
>>>
>>> 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 21:36
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] Secondary structure not visible after
>>> convertingfrom .gro to .pdb
>>>
>>> I am not concerned about secondary structure changes. But I want to
>>> visualize the entire protein structure in ribbon form after energy
>>> minimization... When I see the converted structure (.gro to .pdb) in
>>> pymol,
>>> only one chain is visible. How can I see all the chains together
>>>
>>>
>>> On Thu, May 29, 2014 at 10:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>   [image: Boxbe] <https://www.boxbe.com/overview> This message is
>>> eligible
>>>> for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule<
>>> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DEsaxonTbS0Bg1LbmdB8lfPa4LE7UULWCHdAES9hyLWwbJVgNveMvN1TNzDxkTNeRZq4EELzgfrTs3msZuW4Ire9UausYNhN9r%252FpxIFTZZTlOv39StGyBoEryuoEdnm5zu%252F6hOM5gJh8%253D%26key%3DvMz7TaIDLDZHuZQrXOV4HTpVYbywTj6iPrIoIqnr5LI%253D&tc_serial=17410957201&tc_rand=643677714&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>|
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>>>>
>>>>
>>>>
>>>>
>>>> On 5/28/14, 9:24 PM, bharat gupta wrote:
>>>>
>>>>> 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 ??
>>>>>
>>>>>
>>>> Visualization programs guess what secondary structure should be based on
>>>> the supplied geometry.  Sometimes they get it wrong.  If you're
>>> concerned
>>>> about secondary structure changes, you should be using a quantitative
>>>> method rather than visualization.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
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>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Biomolecular Engineering Laboratory
>>> Pusan National University
>>> South Korea
>>> Mobile no. - 010-5108-3680
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>>
>>
>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

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