[gmx-developers] modify pdb2gmx and/or g_protonate in order to add specific hydrogen name

Emanuel Peter Emanuel.Peter at chemie.uni-regensburg.de
Fri Feb 1 19:40:05 CET 2013

I would try in the hdb entry  

H12A C13 N C12 
H13B C13 N C14
H13C C13 N C15


H12A C13 C12 C14 
H13B C13 C12 C15
H13C C13 N C16

and then afterwards minimize.....

Others might know a better way. 
This way was (for me) the easiest way.
After minimization I got a reasonable protonation.

Best and good luck,


>>> Landry Charlier <landry.charlier at univ-montp1.fr> 02/01/13 12:51 AM >>>


I have some problems in order to automatically add hydrogen to lipids  
with charmm36 force field. Indeed, when several hydrogen have to be  
added to the same atom, the command pdb2gmx -ignh or g_protonate add  
them with the same name but with the last number incremented by 1  
thanks to the .hdb file.

Example :  for charmm36, the hydrogens added to the CB atom of ARG are  
named HB1 & HB2 thanks to the line "2  6  HB  CB  CG  CA" in the  
aminoacids.hdb file.

For lipids, the hydrogen names differ by a letter. H13A, H13B H13C are  
linked to C13 in POPC in charmm36 for example.

I would like to modify g_protonate or pdb2gmx in order to add hydrogen  
with a specific name like that:
- If only 1 name is written in hdb file and several atoms have to be  
added, the hydrogen names have been incremented by 1 as it's by  
default (see the example of Arg above).
- If there are as many names as the number of hydrogen to add, pdb2gmx  
and/or g_protonate will choose these names. The hdb file should be  
like this : 3       4       H13A,H13B,H13C    C13     N       C12

But I check the g_protonate and pdb2gmx files in the source code and I  
am not enough good in programming for modify them.

Could you help me please?


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