This pdb file has 38 models of the trp cage peptide.
Extract model 1:
% convpdb -out ambernoh -model 1 1L2Y.pdb
---- pdb file prints to screen ------
% convpdb -out ambernoh -model 1L2Y.pdb >trp_nmr1.pdb
You will now have a new pdb file with only model one in it. The convpdb.pl tool also renames and reformats pdb files for the needs of different outside programs, CHARMM and Amber predominantly. We ask for amber output here and append the "noh" to tell convpdb.pl to leave out hydrogens. It is best to allow leap to put the hydrogens back in. If you forget the "noh" part of the out specification, then the NMR hydrogens will be preserved but you run the risk of incorrect naming of hydrogens.
Extract the other models from the pdb file.
Use this script (
getmodels.csh) or type it in yourself or just run convpdb.pl 38 times.
#! /bin/csh set i = 0 while( $i < $1 ) @ i = $i + 1 echo $i convpdb.pl -out ambernoh -model $i 1L2Y.pdb > trp_nmr_$i.pdb end |
% enerAmber.pl trp_nmr_1.pdb -422.0600
% enerAmber.pl -out total,bonds,angles,dihedral,impropers,vdwaals,elec,gb,sasa trp_nmr_1.pdb total -422.0600 bonds 8.5460 angles 47.4674 dihedral 0.0000 impropers 0.0000 vdwaals -52.8200 elec -528.3784 gb 0.0000 sasa 0.0000 %
% enerAmber.pl \ -out total,bonds,angles,dihedral,impropers,vdwaals,elec,gb,sasa \ -par param=ff99,gb=tc,cutoff=999 trp_nmr_1.pdb total -630.5800 bonds 8.5460 angles 49.5241 dihedral 0.0000 impropers 0.0000 vdwaals -52.9130 elec -496.2288 gb -321.9512 sasa 0.0000 %