Hi Dan,
Thank you for your reply. Now I am not able to update the AmberTools
because I am not the admin.
I noticed the renumber so I used a same strip in all inputs.
Thank you and look forward to some suggestions.
Best,
Qingfen
Daniel Roe <daniel.r.roe.gmail.com> 于2019年11月21日周四 下午4:52写道：
> 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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> > AMBER.ambermd.org
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>
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Received on Fri Nov 22 2019 - 09:00:02 PST
