Tutorial-l Mailing List

From: Bharath Rajeswaran (bharathrajeswaran_at_gmail.com)
Date: Thu Jun 24 2010 - 07:13:39 CDT

Dear Sir/Madam,

  I am interested in doing simulation of cellulose. I took the Beta D
glucose and since cellulose is a polymer B-D-glucose, I used patches. I was
successfully able to run NAMD for proteins but the above problem created
errors and I tried my best to fix them. I identified in the process a
possible error in the topology file (charmm) that I downloaded from
Meckerell website. In the patch for cellob01, they have given the bond
between 1O4 and 2C1. That's perfect. But they have also bonded 2C1 to 2O5.
2C1 is not an anomeric carbon and only 2C4 should be bonded to 2O5. So
please note this error or correct me if I am wrong.

Thanks for reading.

Regards
Bharath.R

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