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cg topology
- msaeedi
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10 years 8 months ago #1848
by msaeedi
cg topology was created by msaeedi
Hi,
I want to prepare a topology file for a drug molecule in cg model. At first, I maped it in to the beads and guessed bond parameters.
After that, I did the atomistic simulation for this molecule with goromos43a1 force field. I used gromacs version 4.5 software. What do I at a next step?
I used molmaker.py to covert this imperfect topology to cg.gro. can I do a simulation with this and compare it with atomistic simulation?
I looked at Reverse Transformation tutorial in the webpage but I don’t understand that how can I use it for my project?
Please help me in next step to parameterization angle and dihedral parameter for my drug molecule?
I want to prepare a topology file for a drug molecule in cg model. At first, I maped it in to the beads and guessed bond parameters.
After that, I did the atomistic simulation for this molecule with goromos43a1 force field. I used gromacs version 4.5 software. What do I at a next step?
I used molmaker.py to covert this imperfect topology to cg.gro. can I do a simulation with this and compare it with atomistic simulation?
I looked at Reverse Transformation tutorial in the webpage but I don’t understand that how can I use it for my project?
Please help me in next step to parameterization angle and dihedral parameter for my drug molecule?
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- djurre
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10 years 8 months ago #1849
by djurre
Replied by djurre on topic cg topology
Have you read this FAQ:
md.chem.rug.nl/cgmartini/index.php/user-...m/faq#create%20topos
That should answer most of you questions.
md.chem.rug.nl/cgmartini/index.php/user-...m/faq#create%20topos
That should answer most of you questions.
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- nivedita
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10 years 7 months ago #1906
by nivedita
Replied by nivedita on topic cg topology
Dear all,
i used Gromacs 4.5.5 and martini_v2.1 script for protein in water simulation.I did some changes in steps written in tutorial. when i modeled structure by using some other software at that time i already minimized my structure after that i used following step to do cg simulation:
1) ./martinize.py -f model.pdb -x cg.pdb -o system.top -ss model.dssp -p backbone
2) editconf -f cg.pdb -c -d 1.2 -bt cubic -o newbox.gro
3) genbox with vdwd 0.4
4) minimization without position restraint
5) equilibriation nvt followed by npt with postion restraint and integration time dt=20 fs
6) production run without position restraint with dt =20fs
i skip vacuum minimization and energy minimization with position restraint is it ok or i have to follow the steps given in tutorial strictly.
Plz reply ASAP
i used Gromacs 4.5.5 and martini_v2.1 script for protein in water simulation.I did some changes in steps written in tutorial. when i modeled structure by using some other software at that time i already minimized my structure after that i used following step to do cg simulation:
1) ./martinize.py -f model.pdb -x cg.pdb -o system.top -ss model.dssp -p backbone
2) editconf -f cg.pdb -c -d 1.2 -bt cubic -o newbox.gro
3) genbox with vdwd 0.4
4) minimization without position restraint
5) equilibriation nvt followed by npt with postion restraint and integration time dt=20 fs
6) production run without position restraint with dt =20fs
i skip vacuum minimization and energy minimization with position restraint is it ok or i have to follow the steps given in tutorial strictly.
Plz reply ASAP
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- djurre
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10 years 7 months ago #1907
by djurre
Replied by djurre on topic cg topology
I think in general you can skip the vacuum minimization and pr-minimization if it gives you stable simulations.
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- nivedita
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10 years 6 months ago #2439
by nivedita
Replied by nivedita on topic cg topology
Dear All,
I have one doubt, suppose i generate three chain in a protein using SYMMETRY TRANSFORMATIONS information given in crystal structure and all chain are symmetrical due to which when i run ./martinize.py -f model.pdb -x cg.pdb -o system.top -dssp ./dssp-2.0.4-linux-i386 -p backbone
it will generate only one .itp file, and system.top have
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
is it ok or else have to minimize the structure further?
I have one doubt, suppose i generate three chain in a protein using SYMMETRY TRANSFORMATIONS information given in crystal structure and all chain are symmetrical due to which when i run ./martinize.py -f model.pdb -x cg.pdb -o system.top -dssp ./dssp-2.0.4-linux-i386 -p backbone
it will generate only one .itp file, and system.top have
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
is it ok or else have to minimize the structure further?
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- Clement
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10 years 6 months ago #2440
by Clement
Replied by Clement on topic cg topology
I'm not sure what's your point about "minimizing further". Let me get it straight: you have a trimer, and martinize.py does generate a unique .itp file for it. Everything seems in order to me; when you have countless water beads or lipids in your system, you define the respective topologies only once...
[ molecules ]
; name number
Protein_A 3
... would be the right way to do it.
[ molecules ]
; name number
Protein_A 3
... would be the right way to do it.
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- nivedita
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10 years 6 months ago #2441
by nivedita
Replied by nivedita on topic cg topology
Hi clement
All the chain are symmtrical due to which it generate one itp file instead of three itp file for each chain .
my system.top file look like
#include "martini_v2.1.itp"
#include "martini_v2.0_ions.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from trimer.pdb
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
is it fine or something wrong?
All the chain are symmtrical due to which it generate one itp file instead of three itp file for each chain .
my system.top file look like
#include "martini_v2.1.itp"
#include "martini_v2.0_ions.itp"
#include "Protein_A.itp"
[ system ]
; name
Martini system from trimer.pdb
[ molecules ]
; name number
Protein_A 1
Protein_A 1
Protein_A 1
is it fine or something wrong?
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- Clement
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10 years 6 months ago #2476
by Clement
Replied by Clement on topic cg topology
I replied above. YES it is the right way to do it.
You do not need to repeat the statement, and thus:
[ molecules ]
; name number
Protein_A 3
is the way to write it.
You do not need to repeat the statement, and thus:
[ molecules ]
; name number
Protein_A 3
is the way to write it.
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