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

Ali Khan akk5r at virginia.edu
Thu May 29 04:58:17 CEST 2014 

I used to have this problem in pymol as well. When I upgraded pymol to
version 1.7, the problem was fixed and the whole protein would be
displayed.


On Wed, May 28, 2014 at 10:19 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> I checked the structure in VMD, it shows all the chains now but the problem
> is that the entire protein structure is considered as One chain (X)... The
> same is with .gro file i.e. all ten chains are labelled as X...
>
>
> On Thu, May 29, 2014 at 11:11 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%3DhpCDU1npsk4ttShVwJl8TYcbehfZChBDJwpiLmCDUhd0iGEbxjWpz8FtRVnT1vTiBqIRiQOpXsSOF%252FKyDSxUnN4cYOVccMa%252B%252BMMktcZjHYkiAODM0v7fYuK9bKSQP4LHxUo7Ag%252BtlOE%253D%26key%3D2l2bPdZJJzxxH86rgq9BpNMRQ5rMx%252Fj5aZ0wEfrRSgU%253D&tc_serial=17411327790&tc_rand=1534107469&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=17411327790&tc_rand=1534107469&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >
> >
> >
> >
> > 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%3DEsaxonTbS0Bg1LbmdB8lfPa4LE7U
> >>>> ULWCHdAES9hyLWwbJVgNveMvN1TNzDxkTNeRZq4EELzgfrTs3msZuW4Ire9UausYNhN9r%
> >>>> 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>|
> >>>> More
> >>>>
> >>>>> info<
> >>>>>
> >>>> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_
> >>>> serial=17410957201&tc_rand=643677714&utm_source=stf&utm_
> >>>> medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> >>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 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
> >>>>>
> >>>>> ==================================================
> >>>>> --
> >>>>> 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.
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> Bharat
> >>>> Ph.D. Candidate
> >>>> Biomolecular Engineering Laboratory
> >>>> Pusan National University
> >>>> South Korea
> >>>> Mobile no. - 010-5108-3680
> >>>> --
> >>>> 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.
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> > --
> > 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.
> >
> >
>
>
> --
> Bharat
> Ph.D. Candidate
> Biomolecular Engineering Laboratory
> Pusan National University
> South Korea
> Mobile no. - 010-5108-3680
> --
> 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