From: priti arora (priti0806_at_gmail.com)
Date: Fri Aug 03 2007 - 06:10:53 CDT
Hi Shulin
In order to calculate RMSd of C alpha... select trace instead of backbone
in RMSD trajectory tool plugin in VMD
Priti
On 8/3/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
>
> Dear All,
>
> I just do a MD simulations of a small protein using NAMD soft, now, I want
> to calculate the C alpha RMSD of the protein from the trajectory. Using VMD,
> only the backbone RMSD can be calculated.
>
> Another question:
> For hydrogen analysis, how to calculate the hydrogen bond like soft
> PTRAJ. PTRAJ can easily calculate many kind of RMSD from Amber or charmm
> trajectory. How can we use ptraj to analyze trajectory produced by NAMD.
>
> Wish you will give me any help!
> Best regards
> Shulin
>
> --
> Shulin Zhuang, Ph.D.
> Dr. Hongbin Li's group
> Department of Chemistry
> University of British Columbia
> 2036 Main Mall
> Vancouver, BC, Canada V6T 1Z1
> Email: shulin.zhuang_at_gmail.com
>
--
Thanks and regards,
Priti Arora
MSc in Drug Delivery
School of Pharmacy
University of London
Tel: +44 7983024922 (Mob)
+44 2072895561 (Hm)
+44 2077535923 (Lab)
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