AMBER Archive (2004)

Subject: AMBER: Low frequency in quasi-harmonic analysis!!

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Sun May 30 2004 - 04:23:50 CDT

Hi,

  I am doing quasih analysis using AMBER 7. I have 7500 coordinate sets. I am doing it for only the C-alpha atoms of my protein. It seems my frequencies are too low. From 0.290 (lowest)to 1.45 (highest)
Cm-1 for 50 modes.
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My ptraj input is:

trajin je_prodcor_1.mdcrd.gz 1 1250
trajin je_prodcor_3.mdcrd.gz 1 1250
trajin je_prodcor_4.mdcrd.gz 1 1250
trajin je_prodcor_5.mdcrd.gz 1 1250
trajin je_prodcor_6.mdcrd.gz 1 1250
trajin je_prodcor_7.mdcrd.gz 1 1250
strip :WAT
strip @N*
strip @O*
strip @CB*
strip @CD*
strip @CE*
strip @CG*
strip @CZ*
strip @H*
strip @Cl*
strip @C
strip @CH*
strip @S*
rms first :@CA
trajout trunc_out

and my quasih input is;

quasih -natom 190 -nmode 50 -first 1 -last 7500 -m trunc.mass -f 2 < trunc_out > & trunc_quasih &
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Am I doing something wrong?

           Pradipta

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