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normal Connect atoms in different .itp files

  • edroaldo
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11 years 10 months ago #1010 by edroaldo
Connect atoms in different .itp files was created by edroaldo
Dear all,

I have the following problem: I coarse-grain a peptide using the martinize.py script and it worked very well. Thus, I got the .top, .itp and .gro files. However, I have another molecule and so, in another .itp file. I would like to connect some few copies of my CG peptide (file1.itp) to different sites of my molecule defined in another .itp file (file2.itp).

Does someone already experienced this situation before?

Thank you very much!

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11 years 10 months ago #1011 by djurre
Replied by djurre on topic Connect atoms in different .itp files
The best would be if you could combine the peptides and the other molecule in an atomistic pdb and run martinize for the whole system. The bonds between the molecules you can specify with '-link' options.
If that doesn't work, I'm afraid you're up to hand work (or writing a script): combine the separate itp files by copy-pasting and renumber everything.

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11 years 10 months ago #1015 by edroaldo
Replied by edroaldo on topic Connect atoms in different .itp files
Would martinize work with nonstandard martini molecules such as an alkyl thiol, for example?
Thank you very much!

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11 years 10 months ago #1017 by djurre
Replied by djurre on topic Connect atoms in different .itp files
Didn't think about that. No it wont work. But what you could do is change the alkyl thiol by a string of glycines. In the itp file that would give wrong bead types and bonds/angles. But that would be easy to fix. But maybe creating the atomistic pdb would be more work than combining coarse grained itp files.

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11 years 10 months ago #1019 by edroaldo
Replied by edroaldo on topic Connect atoms in different .itp files
Thank you very much for this fast reply. I will write a script to do this task.

Again, thank you very much.

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