Oh,I see.Thanks for your answering!
Liu Wei
On 2014-09-03 18:43, Jason Swails wrote:
> On Wed, Sep 3, 2014 at 5:58 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
>
>> Hi,again
>>
>> I think I met another problem about my topology file. I have tried
>> Dan's
>> suggestion, and I use cpptraj to get the amber topology file named
>> amber.prmtop:
>>
>> parm chamber22gro.prmtop
>> parmwrite out amber.prmtop nochamber
>>
>> And I want to test if these two topology files give the same energy
>> result
>>
>
> No no. They won't. And they're not intended to. The amber.prmtop
> file
> you generated is ONLY for analysis and visualization use. The only
> reason
> this option exists is because some programs do not recognize
> chamber-style
> topology files.
>
> Again: _only_ use the chamber-generated prmtop to actually run
> simulations
> and use the amber.prmtop file for programs that read standard Amber
> topology files but not chamber-style topology files (like ptraj).
>
> HTH,
> Jason
>
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Received on Wed Sep 03 2014 - 05:00:02 PDT
