Dear Baifan,
I saw on amber forum that they sent you the leaprc file, I emailed the
group but no one responded so far. I would highly appreciate if you
would please send that leaprc file to me?
Thank you,
Nihal Korkmaz
On 11/25/14 6:29 AM, Baifan Wang wrote:
> Dear Petr,
>
> Thank you very much for your kind help.
>
> With kind regards,
>
> Baifan
>
> 2014-11-25 10:52 GMT+01:00 Petr Jurecka <jureckap.gmail.com>:
>
>> 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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>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>
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Received on Sun Feb 01 2015 - 11:30:02 PST
