Hi,
First, I recommend upgrading to at least the AmberTools 19 version of
cpptraj (or better yet, the GitHub version:
https://github.com/Amber-MD/cpptraj) - version AT15 is way out of
date.
Second, keep in mind that atoms are renumbered after a "strip" command
- could this be what's going on?
-Dan
On Mon, Nov 18, 2019 at 1:35 PM Q Yu <qfyu2018.gmail.com> wrote:
>
> 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 Thu Nov 21 2019 - 09:00:03 PST
