[gmx-users] Running MD only for selected part of molecule
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 12 13:37:44 CEST 2008
vivek sharma wrote:
> Hi Justin,
> I tried the genpr for generating the posre.itp, but it is taking only a
> single residue while I want to restrict a number of residue for the mdrun.
> Please suggest me the way out.
>
> Procedure followed:
> ....generated gro using pdb2gmx
> ....generated box using editconf
> ....add water using genbox
> ....make pr.index file for the residues I want to restrict for MDS (for
> say 10 residues)
> ....tried genpr command to generate the posre.itp using pr.index
> generated above.
> In th elast step it is generating the posre.itp for a single residue and
> not allowing to include more residues..
> as r_26 in following response..while I want to select all of r_27,28 and 29
>
You need to make these residues a single group. At the make_ndx prompt, you
need to include all the residues you want in that group: r 25-29.
-Justin
>
> Select group to position restrain
> Group 0 ( System) has 23342 elements
> Group 1 ( Protein) has 2626 elements
> Group 2 ( Protein-H) has 2073 elements
> Group 3 ( C-alpha) has 269 elements
> Group 4 ( Backbone) has 807 elements
> Group 5 ( MainChain) has 1077 elements
> Group 6 (MainChain+Cb) has 1329 elements
> Group 7 ( MainChain+H) has 1342 elements
> Group 8 ( SideChain) has 1284 elements
> Group 9 ( SideChain-H) has 996 elements
> Group 10 ( Prot-Masses) has 2626 elements
> Group 11 ( Non-Protein) has 20716 elements
> Group 12 ( NDP) has 61 elements
> Group 13 ( SOL) has 20655 elements
> Group 14 ( Other) has 20716 elements
> Group 15 ( r_25) has 5 elements
> Group 16 ( r_26) has 9 elements
> Group 17 ( r_27) has 5 elements
> Group 18 ( r_28) has 17 elements
> Group 19 ( r_29) has 10 elements
> Select a group: pr
> Error: Multiple groups 'pr' selected
> Error: No such group 'pr'
> Select a group: 16
> Selected 16: 'r_26'
>
> Back Off! I just backed up posre.itp to ./#posre.itp.3#
>
> gcq#232: "These are Ideas, They are Not Lies" (Magnapop)
> _____________________________________________________________
>
> Please suggest
>
> With Thanks,
> Vivek
>
> 2008/10/10 Samuel Coulbourn Flores 花山 <scflores at stanford.edu
> <mailto:scflores at stanford.edu>>
>
> You might want to try Simbody (simtk.org <http://simtk.org>). This
> will allow you to rigidify any part or parts of the molecule you
> choose. As a bonus, you will not spend resources computing
> intramolecular interactions in the rigidified regions.
>
> Sam
>
> On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:
>>
>>
>> vivek sharma wrote:
>>> Hi justin,
>>> My apologies for asking you so many small queries.
>>> Can you suggest any good tutorial or reference that talks about
>>> this issue of running MD over a selected part of molecule.
>>
>> If you're using PR, all you're doing is position-restrained dynamics.
>>
>> -Justin
>>
>>> With Thanks,
>>> Vivek
>>> 2008/10/10 vivek sharma <viveksharma.iitb at gmail.com
>>> <mailto:viveksharma.iitb at gmail.com>
>>> <mailto:viveksharma.iitb at gmail.com>>
>>> hI justin,
>>> Thanks for your response.
>>> do I need to specify the index file(for residue that I want to
>>> keep
>>> fix during MD) during GROMPP or just including the psre.itp in
>>> topology is enough for the purpose ?
>>> With Thanks,
>>> Vivek
>>> 2008/10/10 Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu>>
>>> Justin A. Lemkul wrote:
>>> vivek sharma wrote:
>>> Thanks Justin,
>>> My goal is to keep certain part fixed and move only a
>>> few of the residues (case is like providing
>>> flexibility
>>> to the site of interest only).
>>> SO , do I need to specify the residue using some index
>>> file ?
>>> or is there some other way to specify the part of
>>> molecule for position restraining ??
>>> Make an index file with the residues you want to keep
>>> fixed, and
>>> pass it
>>> to genpr to generate a new posre.itp that corresponds to those
>>> residues.
>>> -Justin
>>> With Thanks,
>>> Vivek
>>> 2008/10/10 Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>
>>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>>>
>>> vivek sharma wrote:
>>> Hi there,
>>> I want to run MD over a part of my molecule ,
>>> for few residues
>>> only (not the whole molecule).
>>> Can I do it using GROMACS ?
>>> I searched for the online documentation and
>>> mailing list, but
>>> unable to get appropriate information.
>>> If somebody has already tried such things
>>> earlier, please
>>> suggest and direct me for appropriate link and
>>> address.
>>> Well, if your goal is to keep certain parts
>>> fixed and
>>> allow others
>>> to move, probably the easiest way to do it is to
>>> apply position
>>> restraints to the "fixed" part.
>>> -Justin
>>> With Thanks,
>>> Vivek
>>> ------------------------------------------------------------------------
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>>> -- ========================================
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu <http://vt.edu>
>>> <http://vt.edu> <http://vt.edu> |
>>> (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> ========================================
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>>> -- ========================================
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>> 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> ========================================
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>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
> Samuel Coulbourn Flores, PhD
> Altman Lab
> Department of BioEngineering
> Stanford University
> samuel.flores at aya.yale.edu <mailto:samuel.flores at aya.yale.edu>
> 650.644.8416
>
> 花山
> 科学者
> 生物工学部
> スタンフォ一ド大学
> スタンフォ一ド、カリフォルニア、米国
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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