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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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Received on Fri Apr 13 2012 - 05:00:05 PDT
