dimer minimisation and psfgen problem

From: Hua Wong (wong_at_ebgm.jussieu.fr)
Date: Wed Mar 17 2004 - 03:17:57 CST

"I maybe wrong but I don't think namd will take more than one psf file."

No, you are not wrong :). Namd will even blurt out an error message specifying that you try to load two structure files.

"In any case you can (and should) combine this file using psfgen. Just
make sure to assign the chains different segment IDs and things will be
fine..."

That's what I want to have help about. I want to run a minimisation on a dimer but I am unsure about how to achieve this...

here is the script I use with psfgen
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
topology top_all22_prot.inp

segment IL8A {
first NONE
last NONE
pdb IL8A.pdb
}

patch DISU IL8A:7 IL8A:34
patch DISU IL8A:9 IL8A:50

coordpdb IL8A.pdb IL8A

writepsf output/IL8A.psf

segment IL8B {
first NONE
last NONE
pdb IL8B.pdb
}

patch DISU IL8B:7 IL8B:34
patch DISU IL8B:9 IL8B:50

coordpdb IL8B.pdb IL8B

writepsf output/IL8B.psf

guesscoord
writepdb output/IL8dimr_out.pdb
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
What do I have to write in order to obtain a single psf with the two segment?

Thanks.

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