Re: pdb and rmsd

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Jan 30 2009 - 21:21:54 CST

Is is fine if atoms belonging to different segments (having differing
segnames) have identical residue (referred to in VMD as either residue or
resid) numbers.

C.

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Fri, Jan 30, 2009 at 1:46 PM, Falgun Shah <fhshah_at_olemiss.edu> wrote:
>
> Dear NAMD user
>
> Hi i am using NAMD for MD simulations. My PDB file has 3 segment. When i
> added water box the water has been added in 4 segment WT1, WT2, WT3 and WT4.
> In addition to it, some residue no. of water molecules are same. Please see
> below:
>
>
> ATOM  24426  H1  TIP3W9261      27.288 -18.939 -13.021  1.00  0.00
> WT1
> ATOM  24427  H2  TIP3W9261      27.886 -20.117 -12.282  1.00  0.00
> WT1
> ATOM  24428  OH2 TIP3W   7      -1.947  33.713 -27.286  1.00  0.00
> WT2
> ATOM  24429  H1  TIP3W   7      -1.514  34.539 -27.070  1.00  0.00
> WT2
> ATOM  24430  H2  TIP3W   7      -2.770  33.739 -26.798  1.00  0.00
> WT2
> ATOM  24431  OH2 TIP3W   8       0.779  17.847  17.918  1.00  0.00
> WT2
>
> Similar resid no:
>
> ATOM  19034  OH2 TIP3W*7056*     -19.057  19.390  -1.922  1.00  0.00
> WT1
> ATOM  19035  H1  TIP3W7056     -18.887  19.411  -0.980  1.00  0.00
> WT1
> ATOM  19036  H2  TIP3W7056     -18.435  18.748  -2.263  1.00  0.00      WT1
>
> ATOM  26291  OH2 TIP3W*7056 *     26.056 -33.151  -1.579  1.00  0.00
> WT2
> ATOM  26292  H1  TIP3W7056      25.973 -32.906  -0.658  1.00  0.00
> WT2
> ATOM  26293  H2  TIP3W7056      27.000 -33.202  -1.729  1.00  0.00
> WT2
>
> Do i need to bother about it.
>
> One more thing! when i did the calculation for RMSD using source rmsd.tcl
>
> the trajectories look distorted (it was fine when i loaded them). Is it
> because of the alignment? but i dont think so.
>
> Please let me know if it is something unusual.
>
> Thanks in advance
>
> --
> Falgun H shah
> PhD candidate (3rd year)
> Department of Medicinal Chemistry
> 2028, Natural Product Center
> University of Mississippi
>
> Ph No: 6629151286(O)
>           662 801 5667(M)
> email: fhshah_at_olemiss.edu
>

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