[gmx-users] Running MD only for selected part of molecule
vivek sharma
viveksharma.iitb at gmail.com
Sun Oct 12 11:39:43 CEST 2008
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
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>
> You might want to try Simbody (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 <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<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 <jalemkul at vt.edu>> <
> mailto:jalemkul at vt.edu <jalemkul at vt.edu>
>
> <mailto:jalemkul at vt.edu <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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> -- ========================================
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> Justin A. Lemkul
>
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>
> Department of Biochemistry
>
> Virginia Tech
>
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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
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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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>
> Samuel Coulbourn Flores, PhD
> Altman Lab
> Department of BioEngineering
> Stanford University
> 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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