On Sat, Mar 27, 2010 at 12:29 AM, Jagdeesh C <jagc666.gmail.com> wrote:
> 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)
ptraj can do this. It is well-documented in the manual.
Good luck,
Jason
>
> %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
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Mar 27 2010 - 08:00:02 PDT
