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From: Qiong Zhang <qiong.zhang.qzh.gmail.com>

Date: Fri, 13 Apr 2012 11:41:05 -0400

Hi Dan,

Yes, I visualized comp-696w.top /comp-696w.mdcrd. It is right that there

are 696 closest waters to the residues 1-390 (in which there are 6028 atoms

in residue 1-390.)

In the PDB file (first.Closest.pdb) produced from cpptraj, there are also

indeed 10 closest waters to the residues 1-390.

So I think in the closestmols.dat, FirstAtm is the atom index for the O in

closest waters, which are exactly 6028, 6031, 6034, ...6055. The reason why

Mol. numbers always 0-9 is that in the comp-696w.mdcrd the water molecules

are already reordered according to their closeness to residue1-390. So it

is always the first 10 water molecules in comp-696w.mdcrd to be selected to

be the closest 10 waters. Is there anything wrong here please?

What I can not understand is the distance values. Why are they zero? What

distance should be in this column please?

Thanks again for your reply!

Qiong

On Fri, Apr 13, 2012 at 9:45 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

*> 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
*

*> >> >> > _______________________________________________
*

*> >> >> > AMBER mailing list
*

*> >> >> > AMBER.ambermd.org
*

*> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >> >>
*

*> >> >> _______________________________________________
*

*> >> >> AMBER mailing list
*

*> >> >> AMBER.ambermd.org
*

*> >> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >> >>
*

*> >> > _______________________________________________
*

*> >> > AMBER mailing list
*

*> >> > AMBER.ambermd.org
*

*> >> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> >> _______________________________________________
*

*> >> AMBER mailing list
*

*> >> AMBER.ambermd.org
*

*> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Fri Apr 13 2012 - 09:00:04 PDT

Date: Fri, 13 Apr 2012 11:41:05 -0400

Hi Dan,

Yes, I visualized comp-696w.top /comp-696w.mdcrd. It is right that there

are 696 closest waters to the residues 1-390 (in which there are 6028 atoms

in residue 1-390.)

In the PDB file (first.Closest.pdb) produced from cpptraj, there are also

indeed 10 closest waters to the residues 1-390.

So I think in the closestmols.dat, FirstAtm is the atom index for the O in

closest waters, which are exactly 6028, 6031, 6034, ...6055. The reason why

Mol. numbers always 0-9 is that in the comp-696w.mdcrd the water molecules

are already reordered according to their closeness to residue1-390. So it

is always the first 10 water molecules in comp-696w.mdcrd to be selected to

be the closest 10 waters. Is there anything wrong here please?

What I can not understand is the distance values. Why are they zero? What

distance should be in this column please?

Thanks again for your reply!

Qiong

On Fri, Apr 13, 2012 at 9:45 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

_______________________________________________

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Received on Fri Apr 13 2012 - 09:00:04 PDT

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