Is it possible to run MD simulations of the protein in a complex with an ssDNA?

More Urszula Sylwia Uciechowska-Kaczmarzyk's questions See All

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How do I prepapre DNA for NAMD simulations?

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How can I determine the Hbond occupancy with GROMACS?

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With regards to Gromacs Radius of gyration, how do I analyse the data?

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fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

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Justin Lemkul

Certainly it is possible.

I don't know that anyone has optimized a force field for ssDNA (probably nonexistent target data), so I would imagine your best bet is a high-quality dsDNA force field.

Grzegorz Wieczorek

It seems that people try to do it with the amber ff. Take a look at http://arxiv.org/abs/1207.5145 .