Dear AMBER list,
I have experienced some issue with cpptraj, when I specify more than 1 parm file. Only the 1st one seems to be used. I tried to carefully follow the syntax of the manual but my 2nd parm file would be ignored. Wonder if something is wrong in my script that I don't see?
An example script of mine looks like this:
parm ../../builtout.gas.pdb [1]
parm ../../1.pdb [2]
trajin 10.align.xtc
reference ../../1.pdb [ref1] parm [2]
reference ../../../native/builtout.gas.pdb [ref2] parm [1]
rms to1 :;176-189&!.H= ref [ref1] nofit out rmsd.out
rms tonative :;176-189&!.H= ref [ref2] nofit out rmsd.out
------------------------------------------------------------------------------
The warning message that would indicate the parm file mismatch issue is as below:
[reference ../../1.pdb [ref1] parm [2]]
Reading '../../1.pdb' as PDB
Read CRYST1 info from PDB: a=56.928 b=70.255 c=55.149 alpha=90 beta=90 gamma=90
Setting active reference for distance-based masks: '1.pdb'
Warning: Active reference has only 4633 atoms, parm 'builtout.gas.pdb' has 4838.
Warning: Parm will only have reference coordinates for the first 4633 atoms (distance-based masks only).
------------------------------------------------------------------------------
So 1.pdb when I use it as my reference file, is still fetching for builtout.gas.pdb the parm [1], instead of parm [2] that I specified. In fact this also would happen in trajectory processing, if I specify different trajectories to different parm files.
This is cpptraj from Amber 22. Any insight would be appreciated, thanks!
J Liao
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Received on Sat Nov 01 2025 - 10:00:02 PDT
