trajectory analysis get error for pdb and dcd file

[imren bayil]

I am using bio3d the first time for my md simulation analysis when I load the my dcd file,

trj <- read.dcd("new1.dcd")
NATOM = 148543
NFRAME= 1002
ISTART= 0
last = 1002
nstep = 1002
nfile = 1002
NSAVE = 1
NDEGF = 0
version 24
|============================================================================| 100%
Warning messages:
1: In readChar(trj, 80) : truncating string with embedded nuls
2: In readChar(trj, 80) : truncating string with embedded nuls
3: In dcd.header(trj, verbose) :
Check DCD header data is correct, particulary natom,I am getting this warning,

When I load the my pdb file;pdb <- read.pdb("step3_input.pdb")
Warning message:
In read.pdb("step3_input.pdb") :
duplicated element numbers ('eleno') detected I am getting this error,especially how to fix pdb error,Could anybody help me please ?

[Xinqiu Yao]

Hi,

The DCD warnings are a bit strange. You might want to check if the file is damaged or generated properly. It is probably fine but better check if the loaded ‘trj’ can be printed properly, has no infinite numbers (e.g., NaN, NA), etc.

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The warning of read.pdb() is fine. It is not an error and you don’t need to worry about it. Simply type pdb to see if the content is appropriate.

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Another thing you might want to check is: If the number of atoms contained in ‘trj’ matches that is shown in ‘pdb’.

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[Xinqiu Yao]

Not a bug.