Dear all,
I am also having trouble setting up a protein+DNA system. I would highly
appreciate if you can email me the relevant files as well, if possible.
Thank you,
Nihal Korkmaz
Biophysics, UW-Madison
On 11/25/14, 3:52 AM, Petr Jurecka wrote:
> Hi Baifan,
>
>
> we will send you the ff99 + bsc0 + ε/ζOL1+ χOL4 leaprc file for Amber 14 to
> your e-mail.
>
>
> Alternatively, you could find the ε/ζOL1 parameters in supporting
> information of Zgarbova et al., JCTC 2013, 9, p2339 and χOL4 parameters in
> Krepl, Zgarbova et al., JCTC 2012, 8, p2506. SI files contain all that is
> necessary to make the ff99 + bsc0 + ε/ζOL1+ χOL4 combination, however, it
> takes some time to make your own leaprc file.
>
>
> Best regards
>
>
> Petr
>
> On Mon, Nov 24, 2014 at 3:55 PM, Baifan Wang <ferlich.comput.gmail.com>
> wrote:
>
>> Dear Amber Users,
>>
>>
>>
>> I currently start to simulate the DNA G-quadruplex. The manual of Amber14
>> recommends that the combination of ff99 + bsc0 + ε/ζOL1+ χOL4 forcefields
>> would have better performance.The manual indicated that, “The appropriate
>> leaprc file will be made available soon as an update to AmberTools.”. My
>> AmberTools has been updated to the nearest version, it seems that the
>> leaprc file is still unavailable. So how can I employ these force field to
>> my simulation?
>>
>>
>>
>> With kind regards,
>>
>>
>>
>> Baifan Wang
>>
>>
>>
>> Kemijski inštitut
>> Ljubljana
>> Slovenija
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>>
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Received on Wed Dec 24 2014 - 20:00:02 PST
