I want to simulate the folding process of two helix proteins in water, but I do not know how to deal with two proteins in CHARMM. For example, there will be only one set of coordinates from the PDB file for each protein, and how will I locate the two proteins? And also, what about some other problems needed to be noticed. Your suggestions are welcome.
In general, folding on the biological or laboratory timescale is beyond the reach of solvated MD simulations using current technology. If the helix is known to associate as a dimer in solution, you may be able to test the relative stability of a series of models using different contact faces between the 2 helices.
Treat each peptide as a separate SEGID, created with independent GENErate commands in CHARMM. Each can be translated and rotated independently by using atom selections with COOR TRANslate and COOR ROTAte commands. For a protein with multiple subunits, it's best to split the PDB file into pieces for each subunit. In this case, because the sequence and initial coordinates for both are the same, one can use duplication commands instead of reading each file separately. A simple example, with comments:
open unit 2 read card name helix.pdb ! OPEN FILE
read sequ pdb unit 2 ! READ AA SEQUENCE
gener A warn ! MAKE FIRST SEGID, A
rewind unit 2 ! REWIND FILE
read coor pdb unit 2 ! READ COORDS
close unit 2 ! CLOSE FILE
hbuild sele atom A * H* end ! BUILD ALL H ATOM COORDS
coor orient ! ALIGN ALONG X AXIS
gener B dupl A ! MAKE 2ND SEGID, B, AS AN EXACT COPY OF A
coor dupl sele segid A end sele segid B end ! COPY COORDS
coor tran ydir 15.0 sele segid A end ! MOVE SEGID A +15 A
coor tran ydir -15.0 sele segid A end ! MOVE SEGID B -15 A