[gmx-users] PROTEIN FOLDING

Thu Dec 28 12:55:49 CET 2017

On 12/28/17 6:25 AM, Neha Gupta wrote:
> I gave
>
> gmx trjconv -pbc nojump -s  prd.gro -f prd.xtc -e 50000.0 -n index.ndx -o
> PRD.pdb
>
> Is there any other alternate command?

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

> Thanks,
> Neha
>
> On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
>> Hi,
>>
>> migh be visualization error
>>
>> Apply pbc
>>
>> On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta <nehaphysics17 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I tried running the simulations for 50 ns.
>>>
>>> The protein breaks (but ligand remains in the active site of the protein
>>> and it is stable throughout )
>>>
>>> How to fix it?
>>>
>>> Thanks,
>>> Neha
>>>
>>> On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
>>> joao.m.a.henriques at gmail.com> wrote:
>>>
>>>> Depends. If you're interested in local folding and there are SS motifs
>> in
>>>> the region you're interested, then yes. If not, no. In terms of overall
>>>> folding of the entire protein, yes it surely can be an important
>>> analysis.
>>>> J
>>>>
>>>> On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysics17 at gmail.com>
>>>> wrote:
>>>>
>>>>> Thank you Joao and Aman.
>>>>>
>>>>> I have noted the points you have suggested.
>>>>>
>>>>> Do you think analyzing DSSP would help?
>>>>>
>>>>> Thanks,
>>>>> Neha
>>>>>
>>>>> On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
>>>>> joao.m.a.henriques at gmail.com> wrote:
>>>>>
>>>>>> "You can use various supporting tools from R language to debug your
>>>>>> trajectory but most third party software support NAMD and charmm
>>>> format.
>>>>>> You can use VMD to convert the trajectory to dcd and use R language
>>>> based
>>>>>> packages to read your trajectory"
>>>>>>
>>>>>> What? How is this useful or helpful? At most it confuses the OP
>> even
>>>>> more.
>>>>>> Also, the clustering analysis is unlikely to be what you want or
>> need
>>>> at
>>>>>> this stage. Why overcomplicate? One of the simplest ways to check
>>> that
>>>>>> there are conformational changes on a given set of atoms is by
>> doing
>>> a
>>>>> RMSD
>>>>>> analysis using the folded structure as the reference. The RMSD is
>>>>> somewhat
>>>>>> degenerate, but should suffice for this purpose. You can use an
>> index
>>>>> file
>>>>>> to restrict the RMSD analysis to a particular subset of your system
>>>> (the
>>>>>> docking site, for example).
>>>>>>
>>>>>> You could look at the radius of gyration as well, Rg, as Aman Deep
>>> also
>>>>>> suggests. This can either be calculated on a subset of atoms or on
>>> the
>>>>>> entire protein. The latter could potentially be used to compare
>> with
>>>> the
>>>>>> experimental reference obtained by SAXS, for example. Or you could
>>>>>> calculate the SAXS curve and get a better understanding of size and
>>>> shape
>>>>>> differences between your protein and the reference, but that's more
>>>>>> advanced stuff.
>>>>>>
>>>>>> J
>>>>>>
>>>>>> On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <
>>> drrahulsuresh at gmail.com
>>>>>> wrote:
>>>>>>
>>>>>>> Also you must know, a lot analysis are available over the entire
>>>> manual
>>>>>> of
>>>>>>> Gromacs where all cannot be performed. Gromacs always provide you
>>> all
>>>>>>> necessary analysis but to choose which one is always your choice
>>> that
>>>>>> suits
>>>>>>> your simulation purpose.
>>>>>>>
>>>>>>>
>>>>>>> On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <
>>> nehaphysics17 at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>>
>>>>>>>> Thank you for your prompt reply.
>>>>>>>>
>>>>>>>> By clustering analysis, are you talking about gmx cluster
>>> command?
>>>>>>>> "over particular PC sub space"
>>>>>>>>
>>>>>>>> Could you please elaborate a bit?
>>>>>>>>
>>>>>>>> Thanks a lot once again.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Neha
>>>>>>>>
>>>>>>>> On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
>>>>> drrahulsuresh at gmail.com
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
>>>>> nehaphysics17 at gmail.com
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi gromacs users,
>>>>>>>>>>
>>>>>>>>>> After MD simulation of protein-ligand complex for 5ns, can
>> we
>>>>> view
>>>>>>>>> protein
>>>>>>>>>> folding?
>>>>>>>>>>
>>>>>>>>>> How to do it?
>>>>>>>>>>
>>>>>>>>>> I want to ascertain if there is any conformation change in
>>>>> protein
>>>>>>>> where
>>>>>>>>>> the ligand binds. Is it possible?
>>>>>>>>>>
>>>>>>>>>> We observe hydrogen bonds through molecular docking.
>> Hence, I
>>>>> want
>>>>>> to
>>>>>>>>> make
>>>>>>>>>> observation through MD simulation which is not obtained
>>> through
>>>>>>>> docking.
>>>>>>>>>
>>>>>>>>> You can perform Clustering analysis over particular PC sub
>>> space
>>>> to
>>>>>>>> measure
>>>>>>>>> the structural changes.
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Can someone help me regarding this?
>>>>>>>>>>
>>>>>>>>>> Thank you very much in advance.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Neha
>>>>>>>>>> --
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>>>>>>>>> --
>>>>>>>>> *Regards,*
>>>>>>>>> *Rahul Suresh*
>>>>>>>>> *Research Scholar*
>>>>>>>>> *Bharathiar University*
>>>>>>>>> *Coimbatore*
>>>>>>>>> --
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>>>>>>>>
>>>>>>> --
>>>>>>> *Regards,*
>>>>>>> *Rahul Suresh*
>>>>>>> *Research Scholar*
>>>>>>> *Bharathiar University*
>>>>>>> *Coimbatore*
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>>
>>
>> --
>> *Regards,*
>> *Rahul Suresh*
>> *Research Scholar*
>> *Bharathiar University*
>> *Coimbatore*
>> --
>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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