[gmx-users] Atom type of hydrogen bonded to aliphatic carbon

Hiromichi Tsurui tsurui at med.juntendo.ac.jp
Fri Dec 2 13:14:01 CET 2005

Dear Gromacs users;
I would like to calculate the effect of mutation by Thermodynamic 
Integration. When editing topology file describing the mutation from Gly (A 
state) to Ala (B state) for example, I must add to topology file a raw 
containing both hydrogen bonded to alpha carbon of Gly (A state) and methyl 
group(CH3) of Ala (B state). However, there is no atom type corresponding to 
hydrogen attached to aliphatic carbon. What atom type should I use for such 
hydrogen ?

Thank you.


Hiromichi Tsurui MD, PhD
Dept. Pathology,
Juntendo University
tsurui at med.juntendo.ac.jp 
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