normal How to add NH2 to carbonyl end group

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3 years 3 months ago - 3 years 3 months ago #4052 by ramadavid
ramadavid created the topic: How to add NH2 to carbonyl end group
Dera Friends ,
I am using thise Martini FF 1st time. I want to 1st thanks to this group for there effort and making the great contribution in the MD field.
My question is I have peptide of eight aminoacid which contain last aminoacid as threonine. The carboxyl group in this free end is blocked by amine group, like CONH2 instead of COOH. When I used the martini.py script I get the following output like :

./martinize.py -f protein.pdb -o system.top -x protein_cg.pdb -ss protein.ssd -p backbone -ff martini22
INFO MARTINIZE, script version 2.4
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 2 chains:
INFO 1: A (Protein), 116 atoms in 8 residues.
INFO 2: A (Unknown), 3 atoms in 1 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Total size of the system: 8 residues.
INFO Will read secondary structure from file (assuming DSSP output).
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Written 1 ITP file
INFO Output contains 1 molecules:
INFO 1-> Protein_A (chain A)
INFO Written topology files
WARNING Martini version 2.2 is in beta release. It has not been extensively tested and problems might occur.
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.

There you are. One MARTINI. Shaken, not stirred.


From this it is clear that end terminal NH2 is not accepted by Martini.
( 2: A (Unknown), 3 atoms in 1 residues. ) This are NH2 residue
So please tell me how to incorporate this in topology ???
How to derived the parameter for this.


And my earnest request to developer to add this modification in new script so we can add methoxy to N-terminal and NH2 to C-terminal ( like gromacs do in selecting terminal option in pdb2gmx command)


please help me in this I will be very thankful for help. I am very naive in deriving the parameters and modification in FF parameter
Last Edit: 3 years 3 months ago by ramadavid.

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9 months 6 days ago - 9 months 6 days ago #7161 by roshanak
roshanak replied the topic: How to add NH2 to carbonyl end group
Hi.
I have a similar question. my peptide has NH2 in c-terminal that is removed by martini. how to add this group?
and another question, I'm simulating 5 peptide with +1 charge in center of membrane that are neutral now (because of removing NH2) and these peptides in the membrane form a pore with all atom scale. but now (with martini) they close the pore. I think, Perhaps this is due to deletion of charge from peptides. Is it true?
I try it with martini 22 force field with and without PME electrostatics and peptides are diverge and pore is closed (1 microseconds). then I do it with martini 22P, polarizable water and PME. this seems peptides begin to aggregate, until this time of simulation (63 ns)
Last Edit: 9 months 6 days ago by roshanak.

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9 months 6 days ago #7162 by peterkroon
peterkroon replied the topic: How to add NH2 to carbonyl end group
Hi,

You'd have to change the type of your C-terminus bead to something like a P5 or Nda (look up a terminal amide in the original Martini papers), and indeed remove the charge.
Note that pore-formation is particularly challenging in Martini, and I'm not surprised to hear your pores collapse.
I don't work with bilayers myself, so I can't help you further...

Peter

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9 months 6 days ago - 9 months 6 days ago #7163 by roshanak
roshanak replied the topic: How to add NH2 to carbonyl end group
thank you
so I must add manually a bead. Isn't a script for this?
Last Edit: 9 months 6 days ago by roshanak.

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9 months 6 days ago #7164 by peterkroon
peterkroon replied the topic: How to add NH2 to carbonyl end group
There's no script for this.

Make the topology with a normal carboxylic acid terminus, and change (not add) that by hand.

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9 months 6 days ago #7165 by Pim
Pim replied the topic: How to add NH2 to carbonyl end group
Yes, Peter is right.
What I do too, as you are not adding any heavy atoms if you amidate the C-terminus (Ominus becomes NH2), is replacing the Qa bead by Nda and of course removing the charge.

In martinize.py there is the option to use neutral termini (flag -nt ), but this will also remove the charge from the N-terminus. In principle you can run martinize with and without -nt and you can manually merge the itp files if you want.

You can get some hints from www.cgmartini.nl/index.php/tutorials-gen...ide#Create-CG-system

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9 months 6 days ago #7166 by roshanak
roshanak replied the topic: How to add NH2 to carbonyl end group
thanks for your answers. I try it.

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9 months 5 days ago - 9 months 5 days ago #7169 by roshanak
roshanak replied the topic: How to add NH2 to carbonyl end group
I changed BB bead (Qa) to (Nda) in itp file and changed -1 charge to 0. then I ran a little minimizatin by grompp for making a new gro file (once I changed my gro file and didn't use from grommp) and when I wanted to make tpr file I saw that charge of protein was 1.000000 . but when I inserted this protein into membrane by insane.py, it shawed charge of protein=0
what should I do? please guide me
Last Edit: 9 months 5 days ago by roshanak.

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9 months 4 days ago #7171 by Pim
Pim replied the topic: How to add NH2 to carbonyl end group
That shouldn't happen, but anyway insane should just create protein/membrane coordinates. In the top file that you use for describing your system and feed to grompp, you simply keep the .itp of your protein and the charge is only read from there. Therefore, if your .tpr is made with a charge of +1, the charge is +1, no matter what insane says.
Also, it's good practice to have charge neutrality in your system, you might want to add a counterion to your box.

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9 months 3 days ago - 9 months 3 days ago #7172 by roshanak
roshanak replied the topic: How to add NH2 to carbonyl end group
thanks for your answer.
I make another tpr after using insan.py and I see charge is 1.000000 yet :)
Last Edit: 9 months 3 days ago by roshanak.

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