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ATP parameters
- yescalona
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11 years 2 days ago #1533
by yescalona
ATP parameters was created by yescalona
I am interested in simulating my protein with ATP
Has anyone developed parameters for ATP?
Where can I find these parameters?
If not, How can I determine these parameters?
Has anyone developed parameters for ATP?
Where can I find these parameters?
If not, How can I determine these parameters?
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- djurre
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11 years 2 days ago #1535
by djurre
Replied by djurre on topic ATP parameters
As far as I know, there are no Martini parameters for ATP. You could make them, below is a short how-to, but it might be a lot of work and for ATP very tricky since it has a lot of charges.
To get parameters you would ideally need an atomistic model and experimental partitioning data.
-The first step is to make a rough first coarse graining scheme: Based on table 3 in Marrink et al., 2007 (doi:10.1021/jp071097f) and some chemical intuition you decide which beads go where on the atomistic structure.
-Second you simulate the atomistic model. Note that it will behave different based on it's enviroment (water, oil, vacuum) and the Martini model probably won't be able to mimick both. You might have to make a choice there.
-Third, based on this atomistic trajectory (say 10ns, but this depends STRONGLY on you molecule) you map this to coarse grain. This can be done using the special version of gromacs (see tutorial part 3, reverse transformation) or using g_traj, or simple to write script. This gives you a "mapped CG trajectory" with beads at the COM positions of the atomistic trajectory. In this trajectory you can measure the bond lengths, angles and dihedrals that will be the target values for your CG.
-Four: create an initial CG itp file with bonds/angles/dihedrals as you get them from step 3 and run a simulation with this CG itp file. Again you measure the bonds/angles/etc. Where they deviate from the goal values, adjust the values in the itp to make them better. Iterate step 4 until you happy.
-Five: Calculate the partitioning free energies of your new itp using Thermodynamic integration/BAR and compare to the experimental value. If the value deviates a bit you can change the bead types you choose in step 1. If it deviates a lot, you might even consider choosing a completely new mapping and start over.
Most of the trouble are likely to appear in step 4. Here are some tips:
-Worse then not getting the right distributions, you might not get a stable simulation at all. In the first steps start at a shorter timestep (1fs?) and try to find out which angles/dihedrals are giving problems. Leave them away for now. Later when you have stable simulation at 20-40 fs you can try switching them back on one by one.
-Often bonded distribution are influenced by non-bonded interactions. Use exclusions!
-Remember you are working on a Coarse Grained topology. The matching of results might be coarse (aka not perfect) as well. This also goes for step 5.
To get parameters you would ideally need an atomistic model and experimental partitioning data.
-The first step is to make a rough first coarse graining scheme: Based on table 3 in Marrink et al., 2007 (doi:10.1021/jp071097f) and some chemical intuition you decide which beads go where on the atomistic structure.
-Second you simulate the atomistic model. Note that it will behave different based on it's enviroment (water, oil, vacuum) and the Martini model probably won't be able to mimick both. You might have to make a choice there.
-Third, based on this atomistic trajectory (say 10ns, but this depends STRONGLY on you molecule) you map this to coarse grain. This can be done using the special version of gromacs (see tutorial part 3, reverse transformation) or using g_traj, or simple to write script. This gives you a "mapped CG trajectory" with beads at the COM positions of the atomistic trajectory. In this trajectory you can measure the bond lengths, angles and dihedrals that will be the target values for your CG.
-Four: create an initial CG itp file with bonds/angles/dihedrals as you get them from step 3 and run a simulation with this CG itp file. Again you measure the bonds/angles/etc. Where they deviate from the goal values, adjust the values in the itp to make them better. Iterate step 4 until you happy.
-Five: Calculate the partitioning free energies of your new itp using Thermodynamic integration/BAR and compare to the experimental value. If the value deviates a bit you can change the bead types you choose in step 1. If it deviates a lot, you might even consider choosing a completely new mapping and start over.
Most of the trouble are likely to appear in step 4. Here are some tips:
-Worse then not getting the right distributions, you might not get a stable simulation at all. In the first steps start at a shorter timestep (1fs?) and try to find out which angles/dihedrals are giving problems. Leave them away for now. Later when you have stable simulation at 20-40 fs you can try switching them back on one by one.
-Often bonded distribution are influenced by non-bonded interactions. Use exclusions!
-Remember you are working on a Coarse Grained topology. The matching of results might be coarse (aka not perfect) as well. This also goes for step 5.
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- castro
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10 years 6 months ago #2148
by castro
Replied by castro on topic ATP parameters
Hi yescalona,
Did you manage to create the ATP cg-model? If so, is it possible to share the the files?
Did you manage to create the ATP cg-model? If so, is it possible to share the the files?
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- siewert
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10 years 6 months ago #2159
by siewert
Replied by siewert on topic ATP parameters
Please note that we are currently parameterizing all nucleosides for their use in DNA and RNA.
I expect to have a beta-release available soon (before the end of the year), that could serve as a perfect base for e.g. ATP.
If you can not wait, please contact me directly (This email address is being protected from spambots. You need JavaScript enabled to view it.) and we can give you a pre-beta release (alpha release?)
I expect to have a beta-release available soon (before the end of the year), that could serve as a perfect base for e.g. ATP.
If you can not wait, please contact me directly (This email address is being protected from spambots. You need JavaScript enabled to view it.) and we can give you a pre-beta release (alpha release?)
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- gskinner
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10 years 3 months ago #3460
by gskinner
Replied by gskinner on topic ATP parameters
I wonder how you are getting along with the parameters for DNA and RNA, I am very interested in trying these out in some protein/DNA systems.
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- prajwal07
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7 years 2 months ago #7001
by prajwal07
Replied by prajwal07 on topic ATP parameters
Hi All,
Does anybody manage to develop parameters for ATP or ADP ? Is it possible to share those parameters.
Thanks and regards
Does anybody manage to develop parameters for ATP or ADP ? Is it possible to share those parameters.
Thanks and regards
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- Carsten
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7 years 2 months ago - 6 years 11 months ago #7073
by Carsten
Replied by Carsten on topic ATP parameters
Hi prawal07,
I recently developed the parameters of ATP and ADP, however, they are not sufficiently tested yet. If you are in hurry, please contact me personally.
I recently developed the parameters of ATP and ADP, however, they are not sufficiently tested yet. If you are in hurry, please contact me personally.
Last edit: 6 years 11 months ago by Carsten.
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- lfhjanssen
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6 years 9 months ago #7312
by lfhjanssen
Replied by lfhjanssen on topic ATP parameters
Hi Carsten, I cannot find any contact information but I am interested in your ATP parameters. Could you email me: This email address is being protected from spambots. You need JavaScript enabled to view it. ? Thank you.
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- SNEHA
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6 years 6 months ago #7406
by SNEHA
Replied by SNEHA on topic ATP parameters
Hi Carsten,
I am interested in simulating system which contains ATP and ADP.
Could you please share the parameter files for MARTINI?
Thanks in advance,
Sneha
I am interested in simulating system which contains ATP and ADP.
Could you please share the parameter files for MARTINI?
Thanks in advance,
Sneha
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- Pim
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6 years 6 months ago #7408
by Pim
Replied by Pim on topic ATP parameters
The best way is to contact Carsten by email, you can find his details here
www.rug.nl/staff/c.f.e.schroer/
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- Carsten
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4 years 1 month ago - 4 years 1 month ago #8460
by Carsten
Replied by Carsten on topic ATP parameters
Dear all,
my parameters of ATP and ADP are published as of today, see
www.pnas.org/content/early/2020/02/28/1914884117
The itp and structure files will soon be provided in the Download section of this website.
Best regards,
Carsten
my parameters of ATP and ADP are published as of today, see
www.pnas.org/content/early/2020/02/28/1914884117
The itp and structure files will soon be provided in the Download section of this website.
Best regards,
Carsten
Last edit: 4 years 1 month ago by Carsten.
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