[gmx-users] A problem about H-bonds

Andrey V Golovin golovin at genebee.msu.su
Thu Jul 29 19:06:38 CEST 2004

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

t> Dear all,
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> 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> Thanks for advance
t> Hailong

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

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