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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!


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"}


$  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,

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

Tel.:  +46 761463349

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