Dear all.
Some typos:
(2) I used the coordinates from (2) -> (2) I used the coordinates from (1)
the relationship between "56121", "7016", and "16677" -> the relationship
between "56121", "7069", and "16677
Thank,
Best,
Yu
Q Yu <qfyu2018.gmail.com> 于2019年11月18日周一 下午6:12写道：
> Dear all,
>
> I used amber15 cpptraj closet to get the first closest water to resides
> 375-383:
> #cpptraj_closest.in
> parm com_solvated_CYX.top
> trajin first.dcd
> strip :Na+
> closest 1 :375-383 first closestout 1_com_solvated_CYX_archive.dat
> outprefix 1_
> trajout 1_com_solvated_CYX.dcd trajectory
>
> The output file "1_com_solvated_CYX_archive.dat" is:
> #CLOSEST_00000[Frame CLOSEST_00000[Mol] CLOSEST_00000[Dist]
> CLOSEST_00000[FirstAtm]
> 1 16677 1.6840
> 56121
>
> I found that "56121" is not an atom of an original solvent molecule
> "16677", by performing the following procedures:
>
> (1) I used the ".top" and ".dcd" obtained from #cpptraj_closest.in to
> output a pdb file,
> #pdb.in
> parm 1_.com_solvated_CYX.top
> trajin 1_com_solvated_CYX.dcd
> strip :Na+
> trajout 1_com_solvated_CYX.pdb pdb
>
> and got the coordinates of the first atom O of the only one water:
> ATOM 6102 O WAT 384 *25.348 1.957 18.311* 1.00 0.00
> O
>
> (2) I used the coordinates from (2) to search the original pdb:
> #pdb_orig.in
> parm com_solvated_CYX.top
> trajin first.dcd
> strip :Na+
> trajout 1_com_solvated_CYX_orig.pdb pdb
>
> and got the coordinates of the water:
> ATOM 56121 O WAT 7069 *25.348 1.957 18.311* 1.00 0.00
> O,
> where "56121" is an atom of "7069" instead of "16677" shown on archive.dat.
>
> I am appreciated if you could provide some information about the
> relationship between "56121", "7016", and "16677"?
>
> Attached are the .dcd and .top.
>
> Thank you.
>
> Best,
>
> Yu
>
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Received on Mon Nov 18 2019 - 11:00:02 PST
