pdb and rmsd

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Fri Jan 30 2009 - 13:46:42 CST

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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