[gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb
bharat gupta
bharat.85.monu at gmail.com
Thu May 29 04:05:24 CEST 2014
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
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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