Modeling Fmoc
- Sofi@
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7 years 1 month ago #7148
by Sofi@
Modeling Fmoc was created by Sofi@
Hi everybody!
I would like to modelize an Fluorenylmethyloxycarbonyl chloride (F-moc) at the end of a oligopeptide. Does anyone have any idea if it has been done before or will I have to modelize it from the begining?
Thanks a lot for the help,
Sofia Bariami
I would like to modelize an Fluorenylmethyloxycarbonyl chloride (F-moc) at the end of a oligopeptide. Does anyone have any idea if it has been done before or will I have to modelize it from the begining?
Thanks a lot for the help,
Sofia Bariami
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- riccardo
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7 years 1 month ago - 5 years 2 weeks ago #7151
by riccardo
Replied by riccardo on topic Modeling Fmoc
Hi,
I don't know of any model for such a molecule, but please check the literature thoroughly.
Otherwise, see tutorials and Martini papers for how to build and validate a model. Here's how I would map it:
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where all but the OCOCl bead are S-beads. S-beads on the aromatic part would be the same as for benzene, so SC5 beads. However, you should also look for experimental partitioning data (also only for fragments of the molecule, in case you don't find data for the whole molecule) against which validate the bead type choices (see tutorials ).
I don't know of any model for such a molecule, but please check the literature thoroughly.
Otherwise, see tutorials and Martini papers for how to build and validate a model. Here's how I would map it:
This image is hidden for guests.
Please log in or register to see it.
where all but the OCOCl bead are S-beads. S-beads on the aromatic part would be the same as for benzene, so SC5 beads. However, you should also look for experimental partitioning data (also only for fragments of the molecule, in case you don't find data for the whole molecule) against which validate the bead type choices (see tutorials ).
Last edit: 5 years 2 weeks ago by riccardo.
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- Pim
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7 years 1 month ago #7152
by Pim
Replied by Pim on topic Modeling Fmoc
Hi Sofia,
Someone affiliated with our group has done some work on Fmoc peptides recently. I will ask him to share his results. Note: the assembly of Fmoc-peptides remained tricky even with the optimized parameters for Martini 2.2.
PS. Thorough atomistic parametrization: pubs.rsc.org/-/content/articlehtml/2016/cp/c5cp06770g
Someone affiliated with our group has done some work on Fmoc peptides recently. I will ask him to share his results. Note: the assembly of Fmoc-peptides remained tricky even with the optimized parameters for Martini 2.2.
PS. Thorough atomistic parametrization: pubs.rsc.org/-/content/articlehtml/2016/cp/c5cp06770g
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- Sofi@
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7 years 1 month ago #7153
by Sofi@
Replied by Sofi@ on topic Modeling Fmoc
Thanks a lot!
Yes, I'm using S beads for sure for the aromatic compound in order to preserve the ring geometry. As for the other part, I hope I'll find something in the literature
:)
Yes, I'm using S beads for sure for the aromatic compound in order to preserve the ring geometry. As for the other part, I hope I'll find something in the literature
:)
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- Sofi@
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7 years 1 month ago #7154
by Sofi@
Replied by Sofi@ on topic Modeling Fmoc
Thank you Pim!
That's very useful :)
That's very useful :)
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- Tomasz
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7 years 1 month ago #7157
by Tomasz
Replied by Tomasz on topic Modeling Fmoc
Dear Sofia,
As Pim mentioned, I've tried to parametrize Fmoc. Unfortunately, my parametrization is not perfect, and it overestimates hydrophobic interactions (experimental logP=1.4 and mine 3.6), so you will need to work a little bit on that. I have used the topology which Riccardo showed. The tricky part was to keep molecule flat - to do that I had to use two virtual sites and bending restriction potential, which requires usage of Gromacs 5. (parameterization is in a similar manner as in this paper: aip.scitation.org/doi/10.1063/1.4937783 )
Below is the topology. For sure it is not perfect, but I think it is a good starting point. You should play more with nonbonded parameters to better reproduce logP. I used timestep 10fs.
Cheers,
Tomasz
[ moleculetype ]
; Name Exclusions
FDP 1
[ atoms ]
1 P5 1 FDP BB 1 0.0000 72.0
2 SC5 1 FDP SC1 2 0.0000 108.0
3 SC5 1 FDP SC2 3 0.0000 0.0
4 SC5 1 FDP SC3 4 0.0000 108.0
5 SC5 1 FDP SC4 5 0.0000 108.0
6 SC5 1 FDP SC5 6 0.0000 108.0
7 SC5 1 FDP SC6 7 0.0000 0.0
[ bonds ]
1 4 1 0.37000 5000 ; FDP
1 5 1 0.36500 9000 ; FDP
[ constraints ]
2 4 1 0.21000 ; FDP
4 5 1 0.19000 ; FDP
5 6 1 0.21000 ; FDP
[ virtual_sites3 ]
3 2 4 5 3 300 0.21000 ; FDP
7 6 5 4 3 300 0.21000 ; FDP
[ angles ]
2 4 5 10 130 200 ; FDP
4 5 6 10 130 200 ; FDP
2 4 1 10 153 100 ; FDP
6 5 1 10 130 100 ; FDP
[ dihedrals ]
2 4 5 6 2 0 50 ; FDP
[ exclusions ]
1 2 3 4 5 6 7
2 3 4 5 6 7
3 4 5 6 7
4 5 6 7
5 6 7
6 7
7
As Pim mentioned, I've tried to parametrize Fmoc. Unfortunately, my parametrization is not perfect, and it overestimates hydrophobic interactions (experimental logP=1.4 and mine 3.6), so you will need to work a little bit on that. I have used the topology which Riccardo showed. The tricky part was to keep molecule flat - to do that I had to use two virtual sites and bending restriction potential, which requires usage of Gromacs 5. (parameterization is in a similar manner as in this paper: aip.scitation.org/doi/10.1063/1.4937783 )
Below is the topology. For sure it is not perfect, but I think it is a good starting point. You should play more with nonbonded parameters to better reproduce logP. I used timestep 10fs.
Cheers,
Tomasz
[ moleculetype ]
; Name Exclusions
FDP 1
[ atoms ]
1 P5 1 FDP BB 1 0.0000 72.0
2 SC5 1 FDP SC1 2 0.0000 108.0
3 SC5 1 FDP SC2 3 0.0000 0.0
4 SC5 1 FDP SC3 4 0.0000 108.0
5 SC5 1 FDP SC4 5 0.0000 108.0
6 SC5 1 FDP SC5 6 0.0000 108.0
7 SC5 1 FDP SC6 7 0.0000 0.0
[ bonds ]
1 4 1 0.37000 5000 ; FDP
1 5 1 0.36500 9000 ; FDP
[ constraints ]
2 4 1 0.21000 ; FDP
4 5 1 0.19000 ; FDP
5 6 1 0.21000 ; FDP
[ virtual_sites3 ]
3 2 4 5 3 300 0.21000 ; FDP
7 6 5 4 3 300 0.21000 ; FDP
[ angles ]
2 4 5 10 130 200 ; FDP
4 5 6 10 130 200 ; FDP
2 4 1 10 153 100 ; FDP
6 5 1 10 130 100 ; FDP
[ dihedrals ]
2 4 5 6 2 0 50 ; FDP
[ exclusions ]
1 2 3 4 5 6 7
2 3 4 5 6 7
3 4 5 6 7
4 5 6 7
5 6 7
6 7
7
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- Sofi@
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7 years 1 month ago #7159
by Sofi@
Replied by Sofi@ on topic Modeling Fmoc
Hi Tomasz,
Thanks a lot for the info. Helped a lot!
Yes I'll check the parameters as you indicated.
Have a good day,
Sofia
Thanks a lot for the info. Helped a lot!
Yes I'll check the parameters as you indicated.
Have a good day,
Sofia
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- rituparna@22
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5 years 2 weeks ago #8079
by rituparna@22
Replied by rituparna@22 on topic Modeling Fmoc
Hello Sir
I am trying to make a martinized coarse grain structure of Phenylalanine with N-terminal capped by Fmoc (Fluorenylmethyloxycarbonyl). I have the .pdb files of all-atom structure required for both PHE and Fmoc and combined them to a single .pdb file. But in martinize.py script, there are only details given for conversion of all-atom to coarse grain structure of PHE. Hence, only coarse grain structure of PHE is being formed and Fmoc is not shown in the martinized output file. Can you please provide the martinize.py script for Fmoc?
I am trying to make a martinized coarse grain structure of Phenylalanine with N-terminal capped by Fmoc (Fluorenylmethyloxycarbonyl). I have the .pdb files of all-atom structure required for both PHE and Fmoc and combined them to a single .pdb file. But in martinize.py script, there are only details given for conversion of all-atom to coarse grain structure of PHE. Hence, only coarse grain structure of PHE is being formed and Fmoc is not shown in the martinized output file. Can you please provide the martinize.py script for Fmoc?
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- riccardo
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5 years 2 weeks ago #8080
by riccardo
Replied by riccardo on topic Modeling Fmoc
Martinize.py will not martinize residues which are not amino acids. Thus, you'll have to merge by hand the PHE and Fmoc models. There's should be enough info in this thread for doing so but let us know if you have some specific doubt.
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5 years 2 weeks ago #8081
by rituparna@22
Replied by rituparna@22 on topic Modeling Fmoc
Hello Sir
How to make coarse grain beads of Fmoc only?
How to make coarse grain beads of Fmoc only?
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- Tomasz
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5 years 2 weeks ago #8082
by Tomasz
Replied by Tomasz on topic Modeling Fmoc
Hi!
Riccardo is right. But, indeed, I do have a modified martnize.py including amino acids and FMoc group. I have not looked at this for quite a while, but it should work. I will post details later.
Cheers,
Tomasz
Riccardo is right. But, indeed, I do have a modified martnize.py including amino acids and FMoc group. I have not looked at this for quite a while, but it should work. I will post details later.
Cheers,
Tomasz
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5 years 2 weeks ago #8083
by rituparna@22
Replied by rituparna@22 on topic Modeling Fmoc
Hi Tomasz,
Can you please help me out with the above said information that you have with you regarding modelling of FMOC with martinize.py? My ongoing project is on hold due to this.
Thanks,
Rituparna
Can you please help me out with the above said information that you have with you regarding modelling of FMOC with martinize.py? My ongoing project is on hold due to this.
Thanks,
Rituparna
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5 years 2 weeks ago #8084
by rituparna@22
Replied by rituparna@22 on topic Modeling Fmoc
The attached file is not opening. Kindly please help me to get the attachment.
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5 years 2 weeks ago #8085
by rituparna@22
Replied by rituparna@22 on topic Modeling Fmoc
I cannot understand the atoms per bead. Please provide me with the necessary information.
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- Tomasz
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5 years 2 weeks ago #8086
by Tomasz
Replied by Tomasz on topic Modeling Fmoc
Hi! Unfortunately, I cannot share all files with you (I do not own rights to part of it) and without them my martinize.py is useless. You have to work than with topology which I post long ago in this thread. Sorry!
Good luck,
Tomasz
Good luck,
Tomasz
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