Dear Amber Developers and Users,
I've been trying to understand why I don't get the same results in the following two cases:
1.) If I use a trajectory rst file (includes a dsDNA dodecamer, Na+ counterions and TIP3P waters; call it 15.rst) and then use the following script in ptraj to center and image the coordinates, everything seems to go smoothly and I get an output PDB file that looks fine in VMD:
trajin 15.rst
trajout 15rstctr.pdb pdb
center :1-24 mass origin
image origin center familiar
2.) On the other hand, if I use a PDB file [made from the same rst file (plus the prmtop file) by using ambpdb (or ptraj); call it 15.pdb] with the following script, again, I successfully get an output PDB file that appears OK in VMD:
trajin 15.pdb
trajout 15pdbctr.pdb pdb
box 55.3927960 55.3927960 55.3927960 109.4712190 109.4712190 109.4712190
center :1-24 mass origin
image origin center familiar
In this second case, the box data is taken to be the six values in the last line of the original rst file.
Here's the problem: the DNA coordinates in the two cases are essentially identical, but the Na+ and WAT coordinates are quite different. Obviously, operator error is involved ;-) somewhere.
Although I've tried a lot of different imaging approaches, the only case where the output PDB files are essentially the same (whether the rst or pdb input file is used) is when I use the fixx, fixy and fixz options (each with value 55.3927960) with the rst file (15.rst). Thus, it appears to me to be related to the box coordinates. I would really appreciate any comments or suggestions.
Thanks in advance,
Bob Hopkins
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Received on Mon Feb 08 2010 - 13:00:03 PST
