Hi Dan,
Thank you for your attention.
I've patched all the bugfixes for AT1.5. I checked the cpptraj tests. They
all passed including the Test_Closest.
This time I fed in a short trajectory with only 5 frames. Now I got all the
outputs.
parm comp-696w.top
trajin comp-696w.mdcrd 1 5 1
closest 10 :1-390 first closestout closestmols.dat outprefix closest
trajout first.Closest.pdb pdb
comp-696w.mdcrd is a trajectory with 696 closest water to residue 1-390
produced by ptraj. With the above script, through cpptraj I got in the
closestmols.dat the following contents:
#Frame Mol Dist FirstAtm
0 0 0.0000 6028
0 1 0.0000 6031
0 2 0.0000 6034
0 3 0.0000 6037
0 4 0.0000 6040
0 5 0.0000 6043
0 6 0.0000 6046
0 7 0.0000 6049
0 8 0.0000 6052
0 9 0.0000 6055
1 0 0.0000 6028
1 1 0.0000 6031
1 2 0.0000 6034
1 3 0.0000 6037
1 4 0.0000 6040
1 5 0.0000 6043
1 6 0.0000 6046
1 7 0.0000 6049
1 8 0.0000 6052
1 9 0.0000 6055
2 0 0.0000 6028
2 1 0.0000 6031
2 2 0.0000 6034
2 3 0.0000 6037
2 4 0.0000 6040
2 5 0.0000 6043
2 6 0.0000 6046
2 7 0.0000 6049
2 8 0.0000 6052
2 9 0.0000 6055
3 0 0.0000 6028
3 1 0.0000 6031
3 2 0.0000 6034
3 3 0.0000 6037
3 4 0.0000 6040
3 5 0.0000 6043
3 6 0.0000 6046
3 7 0.0000 6049
3 8 0.0000 6052
3 9 0.0000 6055
4 0 0.0000 6028
4 1 0.0000 6031
4 2 0.0000 6034
4 3 0.0000 6037
4 4 0.0000 6040
4 5 0.0000 6043
4 6 0.0000 6046
4 7 0.0000 6049
4 8 0.0000 6052
4 9 0.0000 6055
So in the "FirstAtm" column, it is the Index of the O atoms for those
closest waters. And they are ordered according to their closeness to resid
1-390. Am I right?
But why are there all 0.0000 in the Dist column please? What should be the
exact meaning for Dist please? Shouldn't it be the distance of this O atom
to resid 1-390?
Thank you a lot !
Qiong
On Fri, Apr 13, 2012 at 7:33 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It's difficult to know what exactly is going on without more
> information. Can you please provide the exact output cpptraj gives
> (stdout)? Also, do all of the AT1.5 cpptraj test cases pass, and what
> bugfixes (if any) have you applied? Thanks.
>
> -Dan
>
> On Thu, Apr 12, 2012 at 9:29 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>
> wrote:
> > Hi Dan,
> >
> > Yes, I was using ptraj. Thank you for pointing this out.
> >
> > I tried cpptraj with this input:
> >
> > trajin traj.mdcrd 1 5 1
> > trajout test.mdcrd nobox
> > center :1-10 mass origin
> > closest 20 :1-10 first closestout closestout.dat
> >
> > There was no output produced, not even test.mdcrd. With ptraj, at least
> the
> > correct test.mdcrd was produced.
> >
> > Am I missing anything for cpptraj please?
> >
> > Thanks!
> >
> > Qiong
> >
> >
> >
> > On Thu, Apr 12, 2012 at 7:02 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Are you using ptraj? The 'closestout' keyword is only implemented in
> >> cpptraj.
> >>
> >> -Dan
> >>
> >> On Apr 12, 2012, at 5:30 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>
> >> wrote:
> >>
> >> > Hi all,
> >> >
> >> > I am using ambertools1.5 and encountered a problem when using the
> closest
> >> > command. The script I am using is as follows:
> >> >
> >> > trajin traj.mdcrd 1 5 1
> >> > trajout test.mdcrd nobox
> >> > solvent byname WAT
> >> > center :1-10 mass origin
> >> > closest 20 :1-10 first closestout closestout.dat
> >> >
> >> > With this I can obtain the trajectory output test.mdcrd where the 20
> >> > closest waters to residue 1-10 are selected. But no *closestout.dat*
> file
> >> > was produced.
> >> > In the manual it says that " If “closestout” is specified information
> on
> >> > the closest solvent molecules will be print to
> >> > <filename> with format:
> >> > Frame Molecule Distance FirstAtom# "
> >> >
> >> > Could anybody please give me some hint on what might be wrong here
> >> please?
> >> > Thanks!
> >> >
> >> > And if the closestout.dat is produced, what exact content is in this
> file
> >> > please? Will the RESID or AtomID of the closest solvent be given as
> >> > FirstAtom# please?
> >> >
> >> > Qiong
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >>
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Received on Fri Apr 13 2012 - 06:00:07 PDT
