[gmx-users] A problem about H-bonds

[Andrey V Golovin]

Sorry   but standard force field (GMX) does not work well with DNA/RNA
you need to use another ff for you molecule .... wait for week i
think we will publish really checked oplsa parameters for nuclear
acids.

t> Dear all,
t>  
t> I am using GROMACS to analysis my DNA mol, but I have a
t> question can not solve,can you help me ?
t> After I create a dna.pdb file ,I can not make the gromacs konwn
t> where are H-bonds between two residiew , so though i can make the
t> full mdrun ,but there are no h-bond in it .
t>  
t> Another problem is that how can i make the gromacs konwn my H
t> atom in my PDB file if i do not want to use -ignh ?
t>  
t> Thanks for advance
t>  
t> Hailong





-- 
Best regards,
 Andrey                            mailto:golovin at genebee.msu.su