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Topics - oskolkov

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General discussions (Q&As) / Building chromosome with fiber
« on: February 18, 2013, 06:27:50 am »
Dear all,

I would like to ask if anyone tried to build a structure of whole chromosome with fiber? I tried and got a message "allocation failure 1 in cmatrix()", so I suspect that the sequence was too long. Can anyone recommend me how to build a chromosome with fiber or with any other program? Thank you!

Cheers!
Nikolay.

2
MD simulations / How to properly use x3dna_ensemble?
« on: March 22, 2012, 04:59:46 am »
Dear Xiang-Jun and 3DNA users,

I am doing MD simulations of DNA segment using GROMACS 4.0.5 which produces trajectories as xtc and trr files, please find enclosed the initial structure pdb file, I did not manage to attach xtc trajectory (21 Mb) due to size restrictions. I want to analyze the trajectories in order to obtain twist, roll, tilt etc profiles. I found out that x3dna_ensemble script included into x3dna_2.1beta version can provide this information. Unfortunately, I have difficulty running this script and would like to ask you what exactly I should type in my bash in order to analyze my xtc/trr trajectories? For example, I tried

$  x3dna_ensemble convert trajectory.xtc
{:help=>false, :package=>"amber"}

or

$  x3dna_ensemble convert trajectory.xtc -p gromacs
{:help=>false, :package_given=>true, :package=>"gromacs"}

in order to convert MD trajectories to MODEL/ENDMDL format, which can be later analyzed by "x3dna_ensemble analyze", but without success. Do I need to somehow split my xtc/trr trajectory into separate pdb files and apply analyze afterwards? I am completely lost, please help me. Could you please write exact commands I should type in my bash? Thank you.

With best regards,
Nikolay.

**********************************************************************
Dr. Nikolay Oskolkov
Department of Clinical Sciences, Diabetes and Endocrinology,
CRC, Entr 72, building 91, level 12, University Hospital Malmo
SE-205 02 Malmo, Sweden

Email: Nikolay.Oskolkov@med.lu.se
Tel.:  +46 761463349

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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.