Hi,
To perform a SASA calculation on my protein, i tried to remove the Water and ions from my MD simulation using Ptraj:
trajin 2AHI_MD1.mdcrd 1 9999999999 100
strip :WAT
strip :Cl-
strip :Na+
trajout MD_PC_NoWat_test.mdcrd
When i check the result on VMD, there is effectively no more water but the protein structure is totally disturbed, as the atoms tried to take the space left by the water box.
As parameter topology file i tried with the one i used during the MD simulation (including the water box and ions), but i tried also with one without ion and water. Both don't work.
I checked the 2AHI_MD1.mdcrd file, its not the problem.
Can somebody let me know what i am doing wrong?
Thanks,
OZ.
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Received on Sun Oct 16 2011 - 06:30:17 PDT
