Hi,
If you add the .CA it means you're only selecting the alpha carbons of
your residues, and you have to write it both times and the end of your
residue selection. So it should be like this:
distance R1-R2.CA R3.CA out xyz.dat
And that will calculate the distance between the center of mass of R1.CA
and R2.CA to R3.CA. If you want to calculate the center of mass for all
the atoms in the residues, drop the .CA
I'm relatively new to cpptraj, so if I am wrong someone correct me; but
that's how I've been using the distance command for my analysis so far.
Cheers
Juan
On 09/06/15 10:02, Soumendranath Bhakat wrote:
> Dear Juan,
>
> So how it looks
>
> distance R1-R2 R3 .CA out xyz.dat
>
> Does R1-R2 will define the centre between these two residues?
>
> On Tue, Jun 9, 2015 at 10:57 AM, Juan Eiros Zamora <
> j.eiros-zamora14.imperial.ac.uk> wrote:
>
>> My bad,
>>
>> I just saw that you were refering to the center of mass
>>
>> So ignore the 'geom' keyword because that's the default option for cpptraj
>>
>> On 09/06/15 09:55, Juan Eiros Zamora wrote:
>>> Hi,
>>>
>>> You can specify the 'geom' option in the distance command in cpptraj. I
>>> think the following command:
>>>
>>> distance R1-R2 R3 out filename.dat geom
>>>
>>>
>>> should work. You can see the info in section 29.9.19 of the manual
>>>
>>> Cheers
>>> Juan
>>>
>>> On 09/06/15 09:33, Soumendranath Bhakat wrote:
>>>> Dear Amberists,
>>>>
>>>> I have three residues R1, R2 and R3. I wish to calculate the centre of
>> mass
>>>> between R1 and R2 and then calculate distance of R3 from the centre of
>>>> mass.
>>>>
>>>> Can anyone suggest how to do this operation with CPPTRAJ?
>>>>
>>>> Thanks in advance,
>>>>
>>>> /SB
>>>>
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Received on Tue Jun 09 2015 - 02:30:03 PDT
