Hy
I was giving tfollowing the commands
tleap source leaprc.protein.ff14SB MOL=loadpdb 1ua7.pdb savepdb MOL 1ua7-amb.pdb MOL2=loadpdb 1ua7-amb.pdb charge MOL2 source leaprc.water.tip3p solvateBox MOL2 TIP3PBOX 10.0 addIons MOL2 K 14 saveamberparm MOL2 1ua7-wat.prmtop 1ua7-wat.inpcrd
After giving the saveamberparm MOL2 1ua7-wat.prmtop 1ua7-wat.inpcrd .prmtop file is not generated.
How to overcome this problem?
Please help me out.
Remove all lines with "HN" atom from the input PDB file and rerun the command.
[The correct name of hydrogen attached to the backbone nitrogen is "H", not "HN"; tleap ignored "HN" and protonated the backbone nitrogen; therefore, in the output PDB file you have two hydrogens attached to the backbone nitrogen: HN (from the input PDB file) and H (added by tleap).]
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