Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

[SAKO MIRZAIE]

and also this one:

http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/

On 3/31/16, SAKO MIRZAIE  wrote:
> hi
> you can do MD simulation and compute free energy of folding,
> individually. for detect the folding frame or structure, use have to
> regard to RMSD. please look at the following webpage:
>
> http://www3.mpibpc.mpg.de/groups/de_groot/compbio2/p8/index.html
>
> On 3/31/16, Tushar Ranjan Moharana  wrote:
>> Hi SAKO MIRZAIE,
>> Thanks for your reply. But how can we calculate difference in folding
>> free
>> energy by doing 2 separate simulations? Please clarify (at least give
>> some
>> hints or references).
>>
>> Thanks a lot.
>>
>> "A society with free knowledge is better than a society with free food"
>> --
>> Tushar Ranjan Moharana
>> B. Tech, NIT Warangal
>> Ph D Student, CCMB
>> --
>> 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
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a
>> mail to gmx-users-requ...@gromacs.org.
>>
>
>
> --
> ***
> sako mirzaie
> PhD in biochemistry, science faculty, Islamic azad university of
> sanandaj, sanandaj, Iran
> http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie
>
> http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie
>
> http://scholar.google.com/citations?user=viwZvVAJ=en
>
> http://www.scopus.com/authid/detail.url?authorId=54886431500
>
> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
> https://www.researchgate.net/profile/Sako_Mirzaie/publications/
>


-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

[SAKO MIRZAIE]

hi
you can do MD simulation and compute free energy of folding,
individually. for detect the folding frame or structure, use have to
regard to RMSD. please look at the following webpage:

http://www3.mpibpc.mpg.de/groups/de_groot/compbio2/p8/index.html

On 3/31/16, Tushar Ranjan Moharana  wrote:
> Hi SAKO MIRZAIE,
> Thanks for your reply. But how can we calculate difference in folding free
> energy by doing 2 separate simulations? Please clarify (at least give some
> hints or references).
>
> Thanks a lot.
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
> 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-requ...@gromacs.org.
>


-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
-- 
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Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

[Tushar Ranjan Moharana]

Hi SAKO MIRZAIE,
Thanks for your reply. But how can we calculate difference in folding free
energy by doing 2 separate simulations? Please clarify (at least give some
hints or references).

Thanks a lot.

"A society with free knowledge is better than a society with free food"
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
-- 
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Re: [gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation.

[SAKO MIRZAIE]

you can use of swisspdbviewer, discovery studio or any other softer to
do mutation of pdb file. then do MD simulation as a separate protein.

On 3/30/16, Tushar Ranjan Moharana  wrote:
> Hi Everyone,
>
> I want to find the change in delta G between a protein and its mutant (with
> two amino acid mutation). I know for this I have to use "dual topology
> approach" as mentioned in the manual section 5.7.4. I still couldn't get
> how to create such a topology. Is there any direct way (like pdb2gmx or any
> other program). If not then can any body explain me the way to do so(I can
> write perl script if necessary).
>
> Thanks a lot for your time and effort.
>
> "A society with free knowledge is better than a society with free food"
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
> 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
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> mail to gmx-users-requ...@gromacs.org.
>


-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
-- 
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