Dear Amber Users,
I am a bit new to AMBER. I want to find RMSD of very specific atoms from my
prmtop file. I have generated my MDCRD file successfully.
The prmtop file is given below. What is the command I should be using to
find RMSD of these colored red atoms (just an example)
%FLAG
ATOM_NAME
%FORMAT(20a4)
C1 C2 C3 C4 C5 N1 C6 O1 N2 H1 C7 C8 C9 C10 C11 C12 N3 C13 C14
C15
C16 C17 O2 N4 H2 C18 C19 C20 C21 C22 C23 N5 C24 C25 C26 C27 H3 H4 H5
H6
H7 H8 H9 H10 H11 H12 H13 H14 H15 H16 H17 H18 H19 H20 H21 H22 H23 P O1P
O2P
O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 O6 N1 H1 C2
N2
H21 H22 N3 C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4'
O4'
C1' H1' N9 C8 H8 N7 C5 C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 C3' H3'
C2'
H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7
C5
C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P
O5'
C5' H5'1H5'2C4' H4' O4' C1' H1' N1 C6 H6 C5 C7 H71 H72 H73 C4 O4 N3
H3
C2 O2 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1'
H1'
N1 C6 H6 C5 C7 H71 H72 H73 C4 O4 N3 H3 C2 O2 C3' H3' C2'
H2'1H2'2O3'
P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 N6
H61
H62 N1 C2 H2 N3 C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5'
H5'1H5'2C4'
H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 O6 N1 H1 C2 N2 H21 H22 N3 C4
C3'
H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8
H8
N7 C5 C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 C3' H3' C2' H2'1H2'2O3' P
O1P
O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 O6 N1 H1
C2
N2 H21 H22 N3 C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4'
H4'
O4' C1' H1' N1 C6 H6 C5 C7 H71 H72 H73 C4 O4 N3 H3 C2 O2 C3' H3'
C2'
H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N1 C6 H6 C5
C7
H71 H72 H73 C4 O4 N3 H3 C2 O2 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5'
C5'
H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 N6 H61 H62 N1 C2 H2
N3
C4 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1'
N9
C8 H8 N7 C5 C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 C3' H3' C2'
H2'1H2'2O3'
P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N9 C8 H8 N7 C5 C6 O6
N1
Many Thanks,
Jagdeesh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 27 2010 - 01:00:02 PDT
