[gmx-users] PRODRG topology

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Thu Aug 4 17:24:42 CEST 2011

Dear Gromacs Users,

I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this?

Thank you in advance,

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