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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