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protonation states of HISTIDINE
- Chungwen
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11 years 6 months ago #1168
by Chungwen
protonation states of HISTIDINE was created by Chungwen
Is it possible to use HISH instead of HIS in the topology?
I have checked martini_v2.1_aminoacids.itp. There is no options for HISH.
Thanks for the reply.
Chungwen
I have checked martini_v2.1_aminoacids.itp. There is no options for HISH.
Thanks for the reply.
Chungwen
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- djurre
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11 years 6 months ago #1171
by djurre
Replied by djurre on topic protonation states of HISTIDINE
The HISH was originally not parametrized. People have changed one of the P1 beads to a Qd-particle with a plus one charge. I don't know of anything like that has been published.
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- farrotti
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11 years 5 months ago #1287
by farrotti
Replied by farrotti on topic protonation states of HISTIDINE
Hi MARTINI developers,
i have a question on protonaned form of histidine too.
I performed a series of simulations using the 2.P version of the MARTINI FF treating charged form of His residues as described above (i.e. by changing the side-chain SP1 bead to SQd one).
Now, I've just read the article about the new 2.2 version of MARTINI FF ( pubs.acs.org/doi/pdf/10.1021/ct300646g ), in which there is an improvement on the description of charged residues (including His+), and I want to use it for my system.
My question is: how can I build a CG model of His+ in this new FF?
I used the last version of the martinize script (version 2.1), but it doesn't contain the CG mapping of His+, right?
So, I have to manually modify the .top and .gro file, maybe using as reference a Lys residue?
Thank you in advance for your advices,
Andrea Farrotti.
i have a question on protonaned form of histidine too.
I performed a series of simulations using the 2.P version of the MARTINI FF treating charged form of His residues as described above (i.e. by changing the side-chain SP1 bead to SQd one).
Now, I've just read the article about the new 2.2 version of MARTINI FF ( pubs.acs.org/doi/pdf/10.1021/ct300646g ), in which there is an improvement on the description of charged residues (including His+), and I want to use it for my system.
My question is: how can I build a CG model of His+ in this new FF?
I used the last version of the martinize script (version 2.1), but it doesn't contain the CG mapping of His+, right?
So, I have to manually modify the .top and .gro file, maybe using as reference a Lys residue?
Thank you in advance for your advices,
Andrea Farrotti.
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- djurre
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11 years 5 months ago #1288
by djurre
Replied by djurre on topic protonation states of HISTIDINE
The charged histidine is indeed still missing from the martinize-script. We hope we can put a new version online soon, where this will be present. But in the meantime you will have to change the .gro and .top/.itp file by hand. If there are not to many histidines that should not be to much work.
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- farrotti
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11 years 5 months ago #1289
by farrotti
Replied by farrotti on topic protonation states of HISTIDINE
Thanks for the fast reply.
My system contain only a small peptide (26 residue) with 4 His, so I can easily modify the .gro and .top files.
Do you advice me to use the topology of Lys and extend it to His?
I mean, this is the topology I obtained for a Lys residue:
1 Qd 1 LYS BB 1 1.0000 ; H
2 C3 1 LYS SC1 2 0.0000 72.0000 ; H
3 Qd 1 LYS SC2 3 0.0000 36.0000 ; H
4 D 1 LYS SCP 4 1.0000 36.0000 ; H
I have to modify His topology to include in one of side-chain bead the "D" bead? Is it the best way?
Thank you again.
My system contain only a small peptide (26 residue) with 4 His, so I can easily modify the .gro and .top files.
Do you advice me to use the topology of Lys and extend it to His?
I mean, this is the topology I obtained for a Lys residue:
1 Qd 1 LYS BB 1 1.0000 ; H
2 C3 1 LYS SC1 2 0.0000 72.0000 ; H
3 Qd 1 LYS SC2 3 0.0000 36.0000 ; H
4 D 1 LYS SCP 4 1.0000 36.0000 ; H
I have to modify His topology to include in one of side-chain bead the "D" bead? Is it the best way?
Thank you again.
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- djurre
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11 years 5 months ago #1290
by djurre
Replied by djurre on topic protonation states of HISTIDINE
Yes that is probably the best way. Also don't forget to half the masses.
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