Yes, you should use 14SB.
Hai
> On Aug 5, 2015, at 8:59 AM, Mahad Gatti Iou <mahaddino.gmail.com> wrote:
>
> Dear Hai,
>
> so it is enough for simulating RNA and protein together or is better to use
> the ff99SB?
>
> Thanks and regards,
>
> Mahad
>
>
> 2015-08-05 14:48 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
>
>> 'source leaprc.ff14SB' will load protein 14SB ff + DNA bsc0 + RNA chiOL3.
>> You can try can look at the log file from tleap.
>>
>> But I admit that using `ff14SB` name is a bit confusing.
>>
>> Hai
>>
>> On Wed, Aug 5, 2015 at 3:35 AM, Pragya Priyadarshini <pragya.imtech.res.in
>> wrote:
>>
>>>
>>>
>>> Dear Amber users,
>>>
>>> I have to do MD simulation of protein-DNA complex, earlier I have used
>>> ff99SB + bsc0 force field of AMBER11, now I have to use AMBER 14 for my
>>> study. For protein, it is mentioned in AMBER14 manual, to use ff14SB but
>>> I am not getting about DNA. Is ff14SB, sufficient for DNA of protein-DNA
>>> complex or I have to other force field.
>>>
>>> Please suggest me.
>>>
>>> Regards
>>>
>>> --
>>> Pragya Priyadarshini
>>>
>>> C/o Dr. Balvinder Singh
>>> Bioinformatics Center (G N R P C)
>>> Institute of Microbial Technology-CSIR
>>> Sector 39A, Chandigarh-160036, INDIA
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Aug 05 2015 - 06:30:03 PDT
