AMBER Archive (2002)

Subject: secondary structure

From: Ian R Bates (ibates_at_uoguelph.ca)
Date: Tue Mar 26 2002 - 13:49:48 CST

Hello amber users.
        I e-mailed earlier about converting the trajectory history (mdcrd)
to the arc file format familiar to Insight. Thank you to those who
responded.
        I had one more question about determining the percentage of secondary
structure over time from the mdcrd file. The only way I can think of
doing it is by converting the coordinates at each step to pdb then using
dssp to create a hoop load of files with the secondary structure for each
one. Is there a way of using ptraj or carnal for this purpose?
Many thanks
-Ian

 |---------------------------------|\
 | Ian Bates |\
 | Molecular Biology and Genetics |\
 | University of Guelph |\
 | Guelph, Ont., Canada N1G 2W1 |\
 | Email: ibates_at_uoguelph.ca |\
 | Tel: (519)824-4120 ext. 6510 |\
 | FAX: (519)837-2075 |\
 |---------------------------------|\
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