Dear Carlos,
Thanks very much for your comments and the paper. I will then go through
the paper and
do some test runs.
All the best,
Qinghua
On 11/01/2017 03:31 PM, Carlos Simmerling wrote:
> we did some tests in our paper on the GBneck2 model for nucleic acids. Keep
> in mind, though, that energy/force calculations for big systems with
> implicit water can actually be more computationally demanding than in
> explicit water. Carefully benchmark your system to find out.
>
> Refinement of Generalized Born Implicit Solvation Parameters for Nucleic
> Acids and Their Complexes with Proteins
> Nguyen, H., Pérez, A., Bermeo, S., Simmerling, C., Journal of Chemical
> Theory and Computation, 2015, 11 (8), 3714-3728
> DOI: 10.1021/acs.jctc.5b00271
> PMCID: PMC4805114
>
> On Wed, Nov 1, 2017 at 8:15 AM, Qinghua Liao <scorpio.liao.gmail.com> wrote:
>
>> Hello again,
>>
>> Amber ff14SB and Amber DNA bsc1 force fields are used for the protein
>> and the DNA of the complex, respectively, and the complex system with
>> water is very big.
>>
>> I am thinking of performing the simulations in implicit solvents
>> (following simulations with explicit water will also be performed),
>> but I have no experience on it before. Is there someone who did some
>> tests? Any comments or suggestions? Thanks a lot!
>>
>>
>> All the best,
>> Qinghua
>>
>> Hello,
>>
>> I have a complex of a protein and a DNA, and the binding is stable. I am
>> planning to do
>> some pulling simulations along a RMSD, which will be calculated based on
>> the heavy atoms of the
>> DNA after the alignment of the protein. The Amber ff14SB and DNA bsc1
>> force fields were chosen
>> for the protein and DNA, respectively. The purpose of the simulations is
>> to pull the DNA out of the initial binding, and it might
>> find another binding during the pulling. Could someone give me some tips
>> on how to set it up with AMBER?
>> Thanks a lot!
>>
>>
>> All the best,
>> Qinghua
>>
>>
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Received on Wed Nov 01 2017 - 14:30:04 PDT
