TV: 29/10/15

conversion of CG gromacs to AA NAMD
-----------------------------------

CG conversion done within gromacs using modified backward and initram script
- added ASPP as protonated ASP residue

OLD version: system_aa.gro converted into system_aa.pdb and split into domains: protein, membrane + solvent
EDIT: used emst.pdb instead (ensures that all molecules are whole!)
grep SOL emst_center.pdb > system_solvent.pdb
grep 'POP' emst_center.pdb > system_membrane.pdb

problem, as POP represents both POPC and POPG. Conversion made separately into
system_membrane_renum.pdb (renumber indices)
and then sed the correct lipids: system_membrane_renum_sed.pdb

then in vmd:

vmd -dispdev text
package require psfgen

topology ../lib/top_all27_prot_lipid_c36.rtf
segment CTH {pdb system_protein.pdb}
patch ASPP CTH:14
regenerate angles dihedrals
coordpdb system_protein.pdb CTH
guesscoord
writepdb system_protein_out.pdb
writepsf system_protein_out.psf

#restart vmd to load in other rtf, otherwise thinks its a protein -> NH3 added to first POPC :|
mol delete all
resetpsf
topology ../lib/top_all36_lipid.rtf
segment MEM {pdb system_membrane_renum_sed.pdb}
coordpdb system_membrane_renum_sed.pdb MEM
guesscoord
writepdb system_membrane_out.pdb
writepsf system_membrane_out.psf

#How to combine with water? 
#POSSIBILITY 3: #reduce box size! Box too big from CG

mol delete all
resetpsf
mol addfile system_solvent.pdb

#much easier than in the tutorial btw:
set seltext "resname SOL and same residue as abs(z) > 15 and same residue as abs(z) < 100"
set sel [atomselect top $seltext]
$sel writepdb system_solvent_sed.pdb 

pdbalias residue SOL TIP3
pdbalias atom SOL OW OH2
pdbalias atom SOL HW1 H1
pdbalias atom SOL HW2 H2

#renumber residues just to be sure, otherwise complaints about duplicate residues jaddajadda
genconf -f system_solvent_sed.pdb -o system_solvent_sed_genconf.pdb -renumber

#and then also make psf of this
topology ../lib/top_all27_prot_lipid_c36.rtf
mol delete all
resetpsf
pdbalias residue TIP TIP3
segment SOL {
auto none
pdb system_solvent_sed_genconf.pdb
}
coordpdb system_solvent_sed_genconf.pdb SOL
guesscoord
writepdb system_solvent_out.pdb
writepsf system_solvent_out.psf

#and then combine everything!
mol delete all
resetpsf 
readpsf system_protein_out.psf
coordpdb system_protein_out.pdb
readpsf system_membrane_out.psf
coordpdb system_membrane_out.pdb
readpsf system_solvent_out.psf
coordpdb system_solvent_out.pdb
writepsf system_final.psf
writepdb system_final.pdb

#change coordinates of the system:
editconf -f system_final.pdb -o system_finalll.pdb -box 6.5 6.5 8.8
(for TM31C)

#check cellsize of the box
./cellsize.sh system_finalll.pdb

#and minimize with
namd2 ppmini.conf +p 4 > ppmini.log &
(use & to run in background)

then ensure constraints:
add the following part to the config file:
# POSITION RESTRAINTS
# constraints			on
# consref 				restraint.pdb 
# conskfile 			restraint.pdb 
# conskcol 				B 
# constraintScaling 	3.0

# and make restraint.pdb file:
cp mini.coor mini.pdb
mol load psf system.psf pdb mini.pdb 
set case [atomselect top "protein and noh or name P"]
$case set beta 1 
set all [atomselect top all]
$all writepdb restraint.pdb

quit

#and then to hexagon