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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]>>
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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]>>
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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>
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
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Department of Biochemistry
Virginia Tech
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<http://vt.edu> <http://vt.edu> |
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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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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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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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Department of Biochemistry
Virginia Tech
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