TV: 13/12/14

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

CG conversion done within gromacs using backward script

system_aa.gro converted into system_aa.pdb and split into domains: protein, membrane + solvent

chol_new.str downloaded from http://terpconnect.umd.edu/~jbklauda/research/download.html

then in vmd:

cd Documents/noorwegen/results_CG/TM19_cholpopc_backward_namd/systemsetup/

topology ../lib/top_all27_prot_lipid_c36.rtf
segment CTH {pdb system_protein.pdb}
coordpdb system_protein.pdb CTH
guesscoord
writepdb system_protein_out.pdb
writepsf system_protein_out.psf

mol delete all
resetpsf
topology ../lib/top_all36_lipid.rtf
topology ../lib/chol_new.str
pdbalias residue POP POPC
pdbalias residue CLO CHL1
segment MEM {pdb system_membrane.pdb}
coordpdb system_membrane.pdb MEM
guesscoord
writepdb system_membrane_out.pdb
writepsf system_membrane_out.psf

OLD INCORRECT!
segment MEM {
first none
last none
auto none dihedrals
pdb system_membrane.pdb
}


#How to combine with water? 
#POSSIBILITY 3: #reduce box size! Box too big from CG
#went for this option! 
#initial box dimensions: 64.900   64.900  119.043
#final box dimensions of  65.000   65.000   80.000
# so delete water molecules ABOVE and BELOW these, i.e waters between z 0-20 and 100-120

mol delete all
resetpsf
mol addfile system_solvent.pdb

#much easier than in the tutorial btw:
set seltext "resname TIP3 and same residue as abs(z) > 20 and same residue as abs(z) < 100"
set sel [atomselect top $seltext]
$sel writepdb system_solvent_sed.pdb 

#make the following changes in system_solvent_sed.pdb (e.g. with sed or just text editor):
# SOL -> TIP3
# OW -> OH2
# HW1 -> H1
# 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


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

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

#and then to hexagon


#other pretty lame attempts regarding solvent can be found here just for reference:

#POSSIBILITY 1
#stupid vmd cannot read more than 10000 residues, so two separate segments created:
pdbalias residue SOL TIP3
pdbalias atom SOL OW OH2
pdbalias atom SOL HW1 H1
pdbalias atom SOL HW2 H2
segment SOL1 {
auto none
pdb system_solvent.pdb
}
coordpdb system_solvent.pdb SOL
guesscoord
writepdb system_solvent_out.pdb
writepsf system_solvent_out.psf
#does not work

#POSSIBILITY 2
# just resolvate

#first combine prot + membrane from above
mol delete all
resetpsf
readpsf system_protein_out.psf
coordpdb system_protein_out.pdb
readpsf system_membrane_out.psf
coordpdb system_membrane_out.pdb
writepsf system_protein_membrane.psf
writepdb system_protein_membrane.pdb

#then load into vmd
mol delete all
resetpsf
mol new system_protein_membrane.psf
mol addfile system_protein_membrane.pdb
measure minmax [atomselect top all]

#solvate below bilayer
package require solvate
solvate system_protein_membrane.psf system_protein_membrane.pdb -o system_solvate1 -b 1.5 \
-minmax {{0 0 0} {65 65 11}}

mol delete all
resetpsf
mol new system_solvate1.psf
mol addfile system_solvate1.pdb

#solvate above bilayer
package require solvate
solvate system_solvate1.psf system_solvate1.pdb -o system_solvate2 -b 1.5 \
-minmax {{0 0 73} {65 65 80}}
#ERROR! cannot solvate two times apparently due to segment naming :|

#or 
package require solvate
solvate system_protein_membrane.psf system_protein_membrane.pdb -o system_solvate -b 1.5 \
-minmax {{0 0 11} {65 65 73}}

mol delete all
resetpsf
mol new system_solvate.psf
mol addfile system_solvate.pdb

#but here something wrong with selection, also deletes water molecules in the bottom part!
set all [atomselect top all]
$all set beta 0
set seltext "segid WT1 to WT99 and same residue as abs(z) < 36"
set sel [atomselect top $seltext]
$sel set beta 1
set badwater [atomselect top "name OH2 and beta > 0"]
set seglist [$badwater get segid]
set reslist [$badwater get resid]

mol delete all
resetpsf
readpsf system_solvate.psf 
coordpdb system_solvate.pdb
foreach segid $seglist resid $reslist {
        delatom $segid $resid
}
writepdb system_complete.pdb
writepsf system_complete.psf