Good to know! Thank you so much!
On Tue, Jul 30, 2024 at 2:58 PM Carlos Simmerling <
carlos.simmerling.stonybrook.edu> wrote:
> See below
>
> On Tue, Jul 30, 2024, 2:54 PM Quinn Yng <q0001a3.gmail.com> wrote:
>
>> Thanks for the response.
>> I meant to say to adjust the trajectory's protonation states from the
>> cpout files using the server, instead of using it to predict the
>> protonation state.
>> From the scripts (VMD_pH.py) for vmd, it seems like it is selecting the
>> H-atoms that are not present at the frame and moving them further away for
>> visualization purposes.
>> Is there a way to just delete these selected H-atoms?
>> I'm asking because I want to analyze the trajectory ensemble with other
>> tools, and it may have issues with the H-atoms still presented in the frame
>>
>
>
> I think most programs expect the same atoms for each frame. You could do
> this for individual structures, but it's unlikely to be able to use them
> for a single trajectory.
>
> Also, the script takes quite a bit of time. Do you know if I can process
>> the frames with a step size, say once in 100 frames, and only get the
>> trajectory of these frames in VMD?
>>
>
>
>
>> Thank you!
>>
>>
>> On Thu, Jul 25, 2024 at 2:55 PM Carlos Simmerling <
>> carlos.simmerling.stonybrook.edu> wrote:
>>
>>> This is explained in the tutorial on cphmd on the amber web page.
>>>
>>> https://ambermd.org/tutorials/advanced/tutorial18/section4.php
>>>
>>> This is a quite advanced method and you want to really spend time making
>>> sure you understand how it works. For example, the particles representing
>>> thr atoms being titrated are always present in every step of md (but are
>>> sometimes dummy atoms). This is why the trajectory itself does not reflect
>>> the protonation states.
>>> Also, if you use a server to predict the protonation of each frame,
>>> there is little reason to do the constant pH md run.
>>>
>>> On Thu, Jul 25, 2024, 2:29 PM Quinn Yng via AMBER <amber.ambermd.org>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have finished running a constant pH simulation (discrete), and from
>>>> the
>>>> cpout file I know I can obtain the protonation state of each time point
>>>> during the simulation. However, the trajectory doesn't seem to reflect
>>>> the
>>>> protonation states across the simulation.
>>>>
>>>> I would like to analyze the trajectory of the constant ph simulation
>>>> with
>>>> the corresponding protonation states.
>>>> I found servers that can assign protonation states for one pdb, but it
>>>> is
>>>> not able to assign protonation states for multiple pdbs of the
>>>> trajectory
>>>> using the cpout files from the constant pH simulation.
>>>>
>>>> Is there any way to do so?
>>>> Thank you!
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
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Received on Tue Jul 30 2024 - 12:30:02 PDT
