[gmx-users] RE:Interaction Energy

Steven Neumann s.neumann08 at gmail.com
Tue Oct 18 17:43:04 CEST 2011 

On Tue, Oct 18, 2011 at 2:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs <lloyd.riggs at gmx.ch <mailto:
>> lloyd.riggs at gmx.ch>> wrote:
>>
>>    Message: 1
>>    Date: Tue, 18 Oct 2011 06:41:55 -0400
>>    From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>    Subject: Re: [gmx-users] Interaction energy
>>    To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>**>
>>    Message-ID: <4E9D57F3.10905 at vt.edu <mailto:4E9D57F3.10905 at vt.edu>**>
>>
>>    Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>>    Steven Neumann wrote:
>>     >
>>     >
>>     > On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
>>    <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>      > <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>     >
>>     >
>>     >
>>     >     Steven Neumann wrote:
>>     >
>>     >         Dear Gmx Users,
>>     >          I would like to calculate the interaction energy (LJ and
>>     >         electrostatic) between each residue and my ligands (10
>>    ligands
>>     >         in the system). I would like to see what is the
>>    contribution of
>>     >         electrostatic and vdW interactions between ligand and
>>    each of my
>>     >         residue. I thought to use g_energy and specify each of my
>>     >         residues in index files but it is not possible. Will you
>>    suggest
>>     >         how to do this?
>>     >
>>     >
>>     >
>>     >     For such information, you have to specify these groups as
>>    energygrps
>>     >     in the .mdp file.  You can rerun the trajectory using mdrun
>>    -rerun
>>     >     and a new .tpr file specifying these groups, but depending on
>> the
>>     >     output frequency, the result may not be as accurate as you'd
>>    like.
>>     >
>>     >     -Justin
>>     >
>>     >
>>     > Thank you Justin. Now I have two groups sepcified in my mdp file:
>>     >
>>     > energygrps = Protein LIG
>>     >
>>     > How can I specify each residue of my protein separately and each
>>    ligand?
>>     > In my md.gro file I have residues:
>>     >
>>     >     91GLY 92TYR ..... 161LIG 162LIG...
>>     >
>>     >
>>     > Will it be correct like this
>>     >
>>     > energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
>>     >
>>
>>    No.  The names must correspond to valid groups in an index file.
>>
>>     > If yes, will this simulation take longer? Thank you
>>
>>    Perhaps, but certainly your energy file will be considerably larger.
>>
>>    -Justin
>>
>>     >
>>     > Steven
>>     >
>>     >
>>     >
>>     >
>>     >
>>
>>     >--
>>     >=============================**===========
>>
>>    Dear Steven,
>>
>>    I did the following, but like Justin mentioned the files get large.
>>     Basically, I made a very complex ndx file from the beggining.  I
>>    have the whole proteins and peptides involved, then a series of
>>    loops, and protein minus loop, and then individual amino acids and
>>    protein minus the amino acids.  Basically every time you make the
>>    ndx for a particular amino acid/chain/loop you also have to generate
>>    the ndx for the rest of your protein minus what you were looking at.
>>     Otherwise you run out of groups to assign, and will start getting
>>    "residue or atom in multiple groups" when it is referenced more than
>>    one time.
>>
>>    This might not be necessary in your case, but lets you divie up
>>    energy contributions easier, although multiple re-runs using varied
>>    indexes might be necessary, ie for the sum total, then varied parts,
>>    etc...
>>
>>    At least that is a suggestion from my experience..
>>
>>    Freundlichen Grüsse
>>
>>    Stephan Watkins
>>    --
>>    NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
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>>
>>  Thank you Stephan! I have faced the problem you mentioned:
>>  Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 3)
>>  So as I understood what you have written I should specify in my
>> INDEX.ndx:
>>  [r_91] - residue 91
>> 1 2 3.... 7
>> [Protein-r91]  - Protein without residue 91
>> 8 9 10 11... 382
>> [r_92] - resideu 92
>> 8 9 10 11...17
>> [Protein-r92] - Protein without residue 92
>> 1 2..7 18 19 20...38
>>  etc. etc.
>>  And the same with ligands but substracting from my [System] group?
>>
>>
>
> This is not a correct approach, per the fatal error.  If you want to
> monitor energies involving different residues, the only requirement is that
> those residues be in their own distinct groups, i.e.:
>
> energygrps = r_91 r_92 r_93 ... Ligand
>
> The energy groups cannot be redundant.  What Stephan was suggesting is that
> you cannot, for instance, specify:
>
> energygrps = Protein r_91 r_92 ...
>
> because "Protein" encompasses residues 91, 92, etc.  You can, however,
> specify energygrps as in my first example, such that the whole "Protein"
> group is not one of the energygrps.  If you want energies involving those
> residues, you have to do as Stephan suggested and create an "incomplete"
> protein group that excludes the residues that you want to specifically
> analyze.
>
> -Justin
>

Thank you both!!!!

Steven

>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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