Rick, thanks for helps all the way.
My FEP project scale is much smaller. In that case, I may just adjust parameters to fine tuning the water number.
But I am wondering if it is a good way to truncate the water segment by:
1/ partition the whole file into pieces,
2/ and truncate the pdb, and then read them in and generate psf.
for 2/, the read sequ seems work well for pdb, but some times not very compatible with .crd. For example, MG, DNA, ATP, etc. Do you have any idea on that?
3/ is there any better way to do this?