Hi
I can re-frame my query if it was not so clear.
thanks
On Mon, Jun 2, 2014 at 4:36 PM, newamber list <newamberlist.gmail.com>
wrote:
> Hi Daniel
>
>
> Thanks. I used this command:
> nativecontacts :1-356 mindist out mindist.dat
>
> But I have following doubts:
>
> 1) Manual says 'nativecontacts' needs a reference structure so that it
> would mean I need to update reference structure (reference would be the
> same as the frame to be analysed) but in case of distance calculation why
> one would need that?
>
> 2) Also am always getting 0.96 as mindist which I think is the distance of
> hydrogen bonded to some atom (of structure in the unit cell). but I am
> interested in knowing distances of atom pairs with image rather in the unit
> cell itself.
>
>
>
>
>
>
> On Mon, Jun 2, 2014 at 3:50 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> You can use the new 'nativecontacts' command in cpptraj with the
>> 'mindist' keyword to calculate the minimum distance seen either within
>> a single group of atoms or between two groups of atoms. Imaging is on
>> by default for this command when box coordinates are present unless
>> the 'noimage' keyword is specified.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> PS - You can also find the maximum distance with the 'maxdist' keyword.
>>
>> On Mon, Jun 2, 2014 at 8:46 AM, newamber list <newamberlist.gmail.com>
>> wrote:
>> > Hi All
>> >
>> > This is an old mail regarding minimum distance between the images:
>> >
>> > http://archive.ambermd.org/200501/0024.html
>> >
>> > I am just wondering is it implemented now? I need to know the minimum
>> > distance between the images and I can script down to calculate for each
>> > pair of atoms but would be good to know if any inbuilt command can help
>> in
>> > that?
>> >
>> > thanks in advance
>> > JIom
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Jun 04 2014 - 07:30:02 PDT
