Re: atom distances

From: bo baker (bo.bybaker_at_gmail.com)
Date: Wed Jan 04 2006 - 18:09:31 CST

Hi,

I try to use 'ptraj' to extract the distance information. There is one
prolem here. How NAMD mask the atoms in the files of .psf and .dcd? I
tried the way as in Amber, but didn't work. Here is how I did:

ptraj N62-2wation.psf < n62namd-dist1.in

test1:

----
trajin N62-2equil1.dcd.gz
distance a1 out N62-2eq1a.dist  time 0.02 :169_at_OE1 :188_at_NH1
strip :WAT
go
----
The error message:
Mask [:169_at_OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:188_at_NH1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Test2:
----
trajin N62-2equil1.dcd.gz
distance a1 out N62-2eq1a.dist  time 0.02 :1661 :1931
strip :WAT
go
-----
The error message:
Mask [:1661] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:1931] represents 0 atoms !!!NO ATOMS DETECTED!!!
Thanks for any advices.
Bo
On 1/4/06, nmichaud_at_jhu.edu <nmichaud_at_jhu.edu> wrote:
>
> You can use ptraj: http://www.chpc.utah.edu/~cheatham/ptraj.html
>
> ---------------------------------------------------------------------
> Naveen Michaud-Agrawal
> Program in Molecular Biophysics
> Johns Hopkins University
> (410) 614 4435
>
>
> On Wed, 4 Jan 2006, bo baker wrote:
>
> > Hi,   Pijush
> >
> > Thanks for your suggestion. It sounds complicated for me. Is there a
> > simple way to do so? In amber, one can do this with a simple scriple
> > to extract all the distances data from the .crd file (similar to .dcd
> > file in NAMD).
> >
> > > already. Make an indexfile with only those two atoms and then use CATDCD to
> > > extract the trajectories  of those two atoms,
> >
> > > file, and then write a couple of lines prog. either in excel or matlab to
> > > find the distance between the selected atoms over time
> >
> > Could you give me a bit more details about the indexfile? An example
> > would be very helpful.
> >
> > Thank you
> >
> > Bo
> >
> > On 1/4/06, Pijush Ghosh <pijush.ghosh_at_ndsu.edu> wrote:
> > > Hi Bo,
> > >   Its not that difficult. You have your information stored in DCD fileload it in VMD, save it as pdb
> > > file, and then write a couple of lines prog. either in excel or matlab to
> > > find the distance between the selected atoms over time....
> > > Does this work \
> > >
> > > Pijush Ghosh
> > > PhD Student
> > > Department of Civil Engineering
> > > North Dakota State University
> > > Fargo. ND. 58105. USA
> > > Phone:
> > >      701-231-6491(Lab)
> > >      701-231-4341(Res)
> > >
> > > -----Original Message-----
> > > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> > > Of bo baker
> > > Sent: Wednesday, January 04, 2006 2:17 PM
> > > To: namd-l_at_ks.uiuc.edu
> > > Subject: namd-l: atom distances
> > >
> > > Hello, NAMD:
> > >
> > > I would like to exam the distances between two charged atoms from a MD
> > > run. How could I do this? I have search the mail list, and not easy to
> > > find the answer. The VMD can do it by pick up the two targeted atoms.
> > > But how can I get the all the distance value from the trajectories?
> > >
> > > Thank you for your advice.
> > >
> > > Bo
> > >
> > >
> > >
> >
>

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