[gmx-users] protein topology

Nikhil Maroli scinikhil at gmail.com
Tue Oct 27 08:32:06 CET 2015

Dear all,
I wanted to do Protein ligand MD i followed as per the tutorial,when i use
pdb2gmx -f ach.pdb and selecting GROMOS96 43a1 force field
 and SPC water it shows an error
Atom HB1 in residue ASP 5 was not found in rtp entry ASP with 11 atoms
while sorting atoms.
when i checked rtp and input files there is only 9 atoms in rtp so i
couldnt understand what i change i have to make in input files

so i put -ignh flag
it works fine but i need hydrogen atoms
can anyone tell me how to fix it ?

More information about the gromacs.org_gmx-users mailing list