Re: [gmx-users] Protein comparison

2014-11-17 Thread Justin Lemkul 



On 11/17/14 8:09 AM, Onur Tuna wrote:

Dear md,

I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change?

You can perform binding energy calculation, of course. You have a docked
structure. First make sure your docking simulation is reliable. It is
important which software you have used and what kind of protein and ligand
you have. After making sure your docking result is reliable you have to carry
out MD simulation for testing whether your complex structure is stable. From
MD simulations you are able to carry out analysis: what kind of interactions
you have? Charged groups, Hydrogen bonding etc. After making sure your
structure is stable during MD simulation (you can check RMSD values for this)
you are able to calculate Potential of Mean Force using Umbrella Sampling or
you can perform Free Energy Perturbation calculations.



In addition, one must take great care to properly parametrize the ligand for MD 
simulation if the results are to be of any use.


-Justin


Please explore your structure and make sure your docking result is proper
firstly.

Best, Onur


On 17 Nov 2014, at 13:42, rama david  wrote:

Dear MD,


You are asking this question again. but let to tell you, the energy
comparison are made by docking software. Please see the manual of software
and mentioned the name of software you are using.

By gromacs you can do the MD simulation and do analysis of other
interaction pattern.

You cant compare just docking result  in gromacs.




On Mon, Nov 17, 2014 at 9:37 AM, md kashif mailto:kashifzamir180...@gmail.com>> wrote:


Dear all I have protein pdb file and protein+ligand pdb file generated
after docking. How can I compare them by using gromacs? With the word
"compare " I mean that what kind of analysis I can perform? Should I
perform binding energy calculation or rmsd calculation for protein
stability change? Kindly suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:


Dear all I have protein pdb file and protein+ligand pdb file generated
after docking. How can I compare them by using gromacs?

Thanks


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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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Re: [gmx-users] Protein comparison

2014-11-17 Thread Onur Tuna 
Dear md,

I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change?

You can perform binding energy calculation, of course. You have a docked 
structure. First make sure your docking simulation is reliable. It is important 
which software you have used and what kind of protein and ligand you have. 
After making sure your docking result is reliable you have to carry out MD 
simulation for testing whether your complex structure is stable. From MD 
simulations you are able to carry out analysis: what kind of interactions you 
have? Charged groups, Hydrogen bonding etc. After making sure your structure is 
stable during MD simulation (you can check RMSD values for this) you are able 
to calculate Potential of Mean Force using Umbrella Sampling or you can perform 
Free Energy Perturbation calculations.

Please explore your structure and make sure your docking result is proper 
firstly.

Best,
Onur

> On 17 Nov 2014, at 13:42, rama david  wrote:
> 
> Dear MD,
> 
> 
> You are asking this question again. but let to tell you,
> the energy comparison are made by docking software. Please
> see the manual of software and mentioned the name of software you are using.
> 
> By gromacs you can do the MD simulation and do analysis of other
> interaction pattern.
> 
> You cant compare just docking result  in gromacs.
> 
> 
> 
> 
> On Mon, Nov 17, 2014 at 9:37 AM, md kashif  >
> wrote:
> 
>> Dear all
>> I have protein pdb file and protein+ligand pdb file generated after
>> docking. How can I compare them by using gromacs? With the word "compare "
>> I mean that what kind of analysis I can perform? Should I perform binding
>> energy calculation or rmsd calculation for protein stability change? Kindly
>> suggest any tutorial for help.
>> 
>> Thanks
>> 
>> 
>> On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
>> wrote:
>> 
>>> Dear all
>>> I have protein pdb file and protein+ligand pdb file generated after
>>> docking. How can I compare them by using gromacs?
>>> 
>>> Thanks
>>> 
>> --
>> 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.
>> 
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> 
> 
> 
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Re: [gmx-users] Protein comparison

2014-11-17 Thread rama david 
Dear MD,


 You are asking this question again. but let to tell you,
 the energy comparison are made by docking software. Please
see the manual of software and mentioned the name of software you are using.

By gromacs you can do the MD simulation and do analysis of other
interaction pattern.

You cant compare just docking result  in gromacs.




On Mon, Nov 17, 2014 at 9:37 AM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs? With the word "compare "
> I mean that what kind of analysis I can perform? Should I perform binding
> energy calculation or rmsd calculation for protein stability change? Kindly
> suggest any tutorial for help.
>
> Thanks
>
>
> On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
> wrote:
>
> > Dear all
> >  I have protein pdb file and protein+ligand pdb file generated after
> > docking. How can I compare them by using gromacs?
> >
> > Thanks
> >
> --
> 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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Re: [gmx-users] Protein comparison

2014-11-17 Thread Alexander Law 
You need to investigate further for your particular system and the questions 
you want answered. Then come back with specific questions and problems. 

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of md kashif 
[kashifzamir180...@gmail.com]
Sent: Monday, November 17, 2014 5:07 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Protein comparison

Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs? With the word "compare "
I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change? Kindly
suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
>
> Thanks
>
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Re: [gmx-users] Protein comparison

2014-11-16 Thread md kashif 
Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs? With the word "compare "
I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change? Kindly
suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
>
> Thanks
>
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Re: [gmx-users] Protein comparison

2014-11-16 Thread Justin Lemkul 



On 11/16/14 4:43 AM, md kashif wrote:

Dear all
  I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs?



Gromacs is used to perform simulations.  So you need to define what "compare" 
means in terms of something that can be observed using a dynamical simulation.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Protein comparison

2014-11-16 Thread Onur Tuna 
Dear kashifzamir,

What will you compare? As I guess, if you want to compare the protein structure 
before and after docking, you have to use VMD.

Best
Onur

> On 16 Nov 2014, at 11:43, md kashif  wrote:
> 
> Dear all
> I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
> 
> Thanks
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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> mail to gmx-users-requ...@gromacs.org.
> 
> 
> 
> 
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> does not accept any liability for any errors or omissions or any viruses in 
> the context of this message which arise as a result of internet transmission.
> 


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[gmx-users] Protein comparison

2014-11-16 Thread md kashif 
Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs?

Thanks
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