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Messages - Pablo Ricardo Arantes

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1
MD simulations / Runing find_pair to analyze MD trajectory
« on: February 14, 2014, 07:45:23 am »
Hi,

I've a question about when is necessary run find_pair for analyze my MD trajectory in PDB format (output of GROMACS).
I will explain:

1) I always run find_pair for the first frame, I've a PDB file of my first frame. After that, I run analyze with this file.inp for all my MD trajectory in PDB format. It's correct?

2) I was talking with my colleague, and he said I need to generate for every frame of my MD trajectory a new file.inp with find_pair. After that, I run for every frame with different file.inp the analyze program.

I would like to know, what's the correct way to do that??

Thanks for your attention,

Best,

Pablo 

2
RNA structures (DSSR) / Rendering Images of RNA
« on: April 30, 2013, 08:31:18 pm »
Hello!

I work with RNA, and first I would like to thank for dssr program. It's excellent program. Congratulations!!
I would like to know, how can I create a picture with texture on ribbon. If you look at the picture attached, you understood what I'm saying.
I can create images but I can't make a texture on ribbon at Pymol. In picture attached I highlighted what I need.

Thanks!

Best regards.

Pablo Arantes



3
MD simulations / Re: About output files from x3dna_md.rb
« on: September 07, 2012, 10:07:09 pm »
Hi Xiang-Jun,

Thanks for all information! I'm glad that my analysis is fine.
Thanks for advices with the convertion of trajectory and the new version of x3dna_ensemble.

Best regards,

Pablo Ricardo Arantes

4
MD simulations / About output files from x3dna_md.rb
« on: September 07, 2012, 09:23:48 am »
Hello,

I runned the script x3dna_md.rb, and runned everthing fine! But I have some questions about the output files.
1º) The program generated a file, msgfile with these:

......Processing structure #1: <temp_model.inp>......
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name '  C', chain A, number [   1 ]
missing ' O1P' atom : residue name '  C', chain A, number [   1 ]
missing ' O2P' atom : residue name '  C', chain A, number [   1 ]
missing ' P  ' atom : residue name '  U', chain B, number [   1 ]
missing ' O1P' atom : residue name '  U', chain B, number [   1 ]
missing ' O2P' atom : residue name '  U', chain B, number [   1 ]
missing ' P  ' atom : residue name '  C', chain A, number [   1 ]
missing ' P  ' atom : residue name '  U', chain B, number [   1 ]

Time used: 00:00:00:00

Is this normal?

2º) The script generated only two files.out (temp_model.out, my RNA.out). In example folder in the x3dna_md folder, have 4 files .out (x3dna_md.out, x3dna_md2.out, x3dna_md3.out, x3dna_md4.out). I would like to know, If is everything normal with my analysis? The file .out generated, contains the results of all pdb from simulation as a example file.out.

I work in Gromacs program with Amber force field. I converted my trajectory, in separeted pdbs files such as example folder.

Thanks for your attention.

Pablo Ricardo Arantes

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.