[gmx-users] dna topology in OPLS force field

soumadwip ghosh soumadwipghosh at gmail.com
Tue Feb 2 17:53:12 CET 2016

        I am facing some difficulty to simulate single stranded DNA and a
single walled acrbon nanotube. I need different CNTs (with various m and n)
for my study and I am generating them using g_x2top accoring to Andrea
Mineoi's tutorial. It seems to be ok. On the other hand I have to make
topology for ssDNA which I am finding very difficult to generate using OPLS
force field. I tried Topolgen and Topolbuilder both but in the output
topology atomtypes are not defined and the net charge comes out to be zero
which should be -11. My question is is there a possible way to generate
CNTs in combination with CHARMM27 force field with pdb2gmx with all the
dihedral and angle parameters unambiguously. I guess I cannot use g_x2top
in connection with CHARMM. Or is there a way to convert the cnt.top I have
(the OPLS one) into CHARMM atomtypes and parameters? I would appreciate any
insight in this regard. Sorry for asking much.

Thanks and regards,
Soumadwip Ghosh
Senior Research Fellow
IIT Bombay

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