[gmx-users] Converting PDB to gromacs (Hydrogen problems)

[Mark Abraham]

Craig Schwartz wrote:
> Hey Gromacs Users,
>      I am trying to convert the zwitterionic form of glycine into a top 
> and gro file from the pdb, while I appear to be able to do this with 
> some efficiency by PRODRG is there a way to do this that keeps all my 
> hydrogens in the same locations?

Yup. See 
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file 
- you don't ever need to use the coordinate file output from pdb2gmx. 
The necessary and sufficient condition for a successful use of grompp is 
that the ordering of molecules between .top file and coordinate file is 
the same, and within molecules the residue names, atom names and residue 
and atom ordering are identical. Just change any atom & residue names in 
your original .pdb file to agree with the pdb2gmx output names, try 
pdb2gmx on the same file again to verify self-consistency, and use the 
output .top and the input .pdb as input to grompp.

>  This gets more complicated when I try 
> and perform a similar thing on the anion, as I can generate the # of 
> hydrogens etc. but I can't get it to freeze the hydrogen locations.  Is 
> there a way to generate the .gro and .top files directly from a PDB?

Mark