AMBER Archive (2008)

Subject: AMBER: B-factor

From: Furia Gargano (furiagargano_at_gmail.com)
Date: Tue Apr 01 2008 - 14:05:36 CDT

Dear Amber Users,

I`ve calculated the B-factor of my Molecular Dynamic
Simulation with AMBER 9.0 (ff99SB) and I`ve used the script:

reference ../Leap/INHA.pdb
trajin mdcp_teste_fit.crd
rms first out rms_bb_8_10ns.dat :1-268_at_CA,C,N,O
atomicfluct out bf_8_10ns.dat @CA,C,N,O byres bfactor
EOF

The B-factors calculated by AMBER are below experimental ones.

P.S. The B-factor were calculated on the last 2 ns of a 10 ns running.

Thank you very much for your attention.

Best wishes,

Furia

Furia Gargano, Msc
LABIO
PPGCC, PPGBCM & IPB - PUCRS | Fax: +55-51-3320-3621
Av. Ipiranga, 6681
Prédio 32 - Sala 602
90619-900 - Bairro Partenon | E-mail:furiagargano_at_gmail.com
Porto Alegre - RS |
Brasil

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