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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Received on Sun May 30 2004 - 10:53:00 PDT
