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.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.gmail.com
Porto Alegre - RS |
Brasil
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Received on Fri Apr 18 2008 - 21:15:58 PDT
