normal How is the progress on this?

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5 years 3 months ago #3513 by gskinner
How is the progress on this? was created by gskinner
I am really looking forward to trying this out on some systems I am working with? How soon can we expect to see the fruits of your labour on this?

All the best

Count Borgula

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5 years 2 months ago #3584 by jaakko
Replied by jaakko on topic How is the progress on this?
Hi,

the first beta version is now out. I'm sorry it has taken so long.

It's still under development so all feedback is appreciated!

- Jaakko

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5 years 2 months ago - 5 years 2 months ago #3599 by gskinner
Replied by gskinner on topic How is the progress on this?
Thanks for this! I am eager to get this working. Just for clarity, I am not familiar at all with Gromacs and have been using Namd for my CG work. In that past, I have been able to generate NAMD compatible protein files following this tutorial ( www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf‎ ). Now I am trying to apply what I have learned using your new parameters to a short ssDNA oligo. Firstly, I have gotten the new martinize-dna.py script to work on a 20-mer oligo.pdb, resulting in the generation of the files cg-oligo.pdb, oligo.top and oligo_A.itp (chain file?). Now I have a beaded pdb structure of the oligo now (oligo.pdb) but for NAMD I need to generate a .psf file (the topology?). For the protein tutorial this involved using the AUTOpsf tool in VMD along with the martini-protein.top file. The .top file generated by your script does not work for this, and opening up it it only says the following.


"#include "martini.itp"



#include "Oligo_A.itp"

[ system ]
; name
Martini system from Oligo.pdb

[ molecules ]
; name number
Oligo_A 1"

I know you have focused your development on Gromacs (and perhaps this the other route I should go to get this to work), but can you help me to get this work at all with NAMD? Many sincere thanks. Gary
Last edit: 5 years 2 months ago by gskinner. Reason: Wrong filenames

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5 years 2 months ago #3604 by jaakko
Replied by jaakko on topic How is the progress on this?
Hi Gary,

I haven't used NAMD so I can't help much with that part. But I can help with the martinize part, I'm guessing the difference is that in the previous one the molecule was defined inside the .top file. The #include statement can be repalced by copypasting the contents of the particular file into the .top file. I hope doing that will make the NAMD tool work.

Another thing, you renamed the molecule to Oligo_A, right? Did you change that also inside the Oligo_A.itp file?

- Jaakko

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