Hi,
Have you tried visualizing your topology and trajectory (comp-696w.top
/ comp-696w.mdcrd)? According to this output your first molecule has
an atom # of 6028, which doesn't seem right. This combined with the
zero values in the distance column, as well as the repeating sequence
of closest molecules (always 0 to 9), makes me think that something
has gone wrong with either the topology, the trajectory, or both. Note
that in the output from cpptraj 'closest closestout' both atom #s and
molecule numbers start from 0.
-Dan
On Fri, Apr 13, 2012 at 8:51 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com> wrote:
> 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
>> >> > _______________________________________________
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>> >>
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Received on Fri Apr 13 2012 - 07:00:05 PDT
