[gmx-users] regarding pdb2gmx

soumadwip ghosh soumadwipghosh at gmail.com
Sat May 30 16:24:35 CEST 2015

Thanks Justin for your insights.

So when I am making the topology of DNA via ppdb2gmx using CHARMM, the
parameters in the .itp files are not adequate and I should place them
manually everytime I make a molecule topology with pdb2gmx? In some of
my previous works actually the DNA molecule gave outcomes which were
pretty much expected. So, just like I have put all the missing
parameters in the .cnt.itp file should I do the same with the dna.itp
generated by pdb2gmx in order to ensure correct interactions?

thanks for your time in advance

Research Fellow

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