Hi
Your plot is not coming through, not sure why. Without it, it would be
hard to tel you what is going on.
Adrian
On 12/23/20 10:44 AM, Sruthi Sudhakar wrote:
> [External Email]
>
> Sir,
> Sorry for the confusion. It is a distance plot between the N+ atom and
> phosphate of the backbone. These are expected to show electrostatic
> interactions since the backbone is negative. The script we have used for
> this calculation is
> parm comsol.prmtop
> trajin prod.nc
> rms first :1-23
> distance :14.OP2 :1.N4 out distance4_14_OP2.dat
>
> And I got the plot attached. But the value ranges in between 2-20
> angstroms. Is it likely to have such values ?
>
> Regards,
> Sruthi Sudhakar
>
>
> On Wed, Dec 23, 2020 at 8:34 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> I think it was confusing that you said it was an "electrostatic distance
>> plot" but really this is just a distance plot. If you are looking to
>> analyze hydrogen bonds, cpptraj has that ability and can provide much more
>> detailed information that seen in your distance plot. The cpptraj manual
>> has details, and there are tutorials available.
>>
>> On Wed, Dec 23, 2020 at 9:19 AM Sruthi Sudhakar <
>> sruthisudhakarraji.gmail.com> wrote:
>>
>>> Dear prof. Case,
>>> The cut off merely means that in the plot if the distance of 3.5
>> angstroms
>>> or less is maintained, it was considered to be a good electrostatic
>>> interaction in the system throughout the simulation. This notion was
>>> considered referring some previous publications. Hope the attachment is
>> now
>>> visible to you.
>>>
>>>
>>> On Wed, 23 Dec 2020 at 7:38 PM, David A Case <david.case.rutgers.edu>
>>> wrote:
>>>
>>>> On Wed, Dec 23, 2020, Sruthi Sudhakar wrote:
>>>>
>>>>> I have been calculating the electrostatic distance plot between the
>>>>> protonated nitrogen atom of my ligand and the negatively charged
>>> backbone
>>>>> of DNA in a DNA-ligand complex. The distance was calculated using the
>>>>> distance option in cpptraj. The protonated nitrogen belongs to the
>>>>> pyrrodiline ring at the end of a propyl chain. The plot between the N+
>>> and
>>>>> OP is attached here. If the cut off of 3.5 angstroms is considered
>> are
>>>> the
>>>>> high fluctuations (10-20 angstroms) seen in the plot possible or is it
>>>> some
>>>>> discrepancy? Kindly advise on the above.
>>>> Nothing was attached...you might also be more specific about what you
>>>> mean a "cut off of 3.5 angstroms"....
>>>>
>>>> ....dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=KpjIauOydynzumpJJZ3HsjCEMs4mWXzy_LsknwyMJfc&s=gnI4k1lum9CI7WOfx--NOdoT0yGSJIPV03aNwPjwTg8&e=
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=KpjIauOydynzumpJJZ3HsjCEMs4mWXzy_LsknwyMJfc&s=gnI4k1lum9CI7WOfx--NOdoT0yGSJIPV03aNwPjwTg8&e=
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=KpjIauOydynzumpJJZ3HsjCEMs4mWXzy_LsknwyMJfc&s=gnI4k1lum9CI7WOfx--NOdoT0yGSJIPV03aNwPjwTg8&e=
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=KpjIauOydynzumpJJZ3HsjCEMs4mWXzy_LsknwyMJfc&s=gnI4k1lum9CI7WOfx--NOdoT0yGSJIPV03aNwPjwTg8&e=
--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 23 2020 - 08:00:03 PST
