Hello all..
I am trying to carry out some pca analysis and am doing some preparatory
work in ptraj. I am interested in my active site residues, and then in the
CA atoms of my active site residues. I prepared two sets of command lines as
follows:
PTRAJ 1 Active Site RESIDUES
trajin /DATA/1e3g_wat_md2.mdcrd.gz
trajin /DATA/1e3g_wat_md3.mdcrd.gz
trajin /DATA/1e3g_wat_md4.mdcrd.gz
trajin /DATA/1e3g_wat_md5.mdcrd.gz
trajin /DATA/1e3g_wat_md6.mdcrd.gz
trajin /DATA/1e3g_wat_md7.mdcrd.gz
trajin /DATA/1e3g_wat_md8.mdcrd.gz
trajin /DATA/1e3g_wat_md9.mdcrd.gz
trajin /DATA/1e3g_wat_md10.mdcrd.gz
rms first out /DATA/undocked_rms1_as.out
:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
average /DATA/undocked_average_output_as.pdb pdb nowrap
go
PTRAJ2 Active Site RESIDUES
trajin /DATA/1e3g_wat_md2.mdcrd.gz
trajin /DATA/1e3g_wat_md3.mdcrd.gz
trajin /DATA/1e3g_wat_md4.mdcrd.gz
trajin /DATA/1e3g_wat_md5.mdcrd.gz
trajin /DATA/1e3g_wat_md6.mdcrd.gz
trajin /DATA/1e3g_wat_md7.mdcrd.gz
trajin /DATA/1e3g_wat_md8.mdcrd.gz
trajin /DATA/1e3g_wat_md9.mdcrd.gz
trajin /DATA/1e3g_wat_md10.mdcrd.gz
reference /DATA/undocked_average_output_as.pdb
rms first out /DATA/undocked_rms2_as.out
:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
strip
~:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
trajout /DATA/undocked_rms2.out_as.mdcrd
go
PTRAJ 1a Active Site RESIDUES CA ONLY
trajin /DATA/1e3g_wat_md2.mdcrd.gz
trajin /DATA/1e3g_wat_md3.mdcrd.gz
trajin /DATA/1e3g_wat_md4.mdcrd.gz
trajin /DATA/1e3g_wat_md5.mdcrd.gz
trajin /DATA/1e3g_wat_md6.mdcrd.gz
trajin /DATA/1e3g_wat_md7.mdcrd.gz
trajin /DATA/1e3g_wat_md8.mdcrd.gz
trajin /DATA/1e3g_wat_md9.mdcrd.gz
trajin /DATA/1e3g_wat_md10.mdcrd.gz
rms first out /DATA/undocked_rms1_as_CA.out
:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231.CA
average /DATA/undocked_average_output_as_CA.pdb pdb nowrap
go
PTRAJ 2a Active Site RESIDUES CA ONLY
trajin /DATA/1e3g_wat_md2.mdcrd.gz
trajin /DATA/1e3g_wat_md3.mdcrd.gz
trajin /DATA/1e3g_wat_md4.mdcrd.gz
trajin /DATA/1e3g_wat_md5.mdcrd.gz
trajin /DATA/1e3g_wat_md6.mdcrd.gz
trajin /DATA/1e3g_wat_md7.mdcrd.gz
trajin /DATA/1e3g_wat_md8.mdcrd.gz
trajin /DATA/1e3g_wat_md9.mdcrd.gz
trajin /DATA/1e3g_wat_md10.mdcrd.gz
reference /DATA/undocked_average_output_as.pdb
rms first out /DATA/undocked_rms2_as_CA.out
:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231.CA
strip
~:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231.CA
trajout /DATA/undocked_rms2.out_as_CA.mdcrd
go
In the first set PTRAJ 1 & 2 I am working on the entire amino acids making
up the active site. In the second set PTRAJ 1a & 2a I am working on the
alpha carbons of the amino acids making up the active site. For both cases,
in ptraj 1 I generate an average pdb for my trajectory, which acts as a
reference in ptraj 2 when I fix each trajectory frame to the first (or
reference). I must have some problem in assigning my mask, because when I
continue further I get error messages. In PTRAJ 1 & 2 I am selecting for the
residues hence the use of :33,36,37 etc and then in PTRAJ 1a & 2a I am
selecting for the CA of these residues- hence the .CA after the residues
being considered.
Can anyone tell me what is wrong with my script files please?
Thanks in advance
claire
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Received on Sun Mar 05 2006 - 06:10:10 PST
