[gmx-users] choice of the hydrogen name added thanks to .hdb file ?

Landraille landry.charlier at univ-montp1.fr
Thu Jan 31 18:25:30 CET 2013


I would like to know if it's possible to give a specific name to an hydrogen
which will be added thanks to the .hdb file. 
Indeed, by default, the hydrogens added on the same carbon have the same
name with the last number incremented by 1. 
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

But if I want the names H1A & H1B ? If i write the lines "2  6  H1  CB  CG
 CA" in the aminoacids.hdb file, the hydrogens will have the names H11 &

I ask this question because I would like to add hydrogens to lipids
automatically and the difference between hydrogens on the same atom depends
of a letter and not a number in charmm36. (H13A, H13B H13C are linked to C13
in POPC for example) 

Thank you.

View this message in context: http://gromacs.5086.n6.nabble.com/choice-of-the-hydrogen-name-added-thanks-to-hdb-file-tp5005051.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list