I strongly recommend using the most recent version of AmberTools. That said, the only reason I can think of that would cause a difference is that min.rst is in ncrst format. If you *need* to use AmberTools 16, try converting it to nc format:
cpptraj -p input.top -y min.rst -x min.nc
I don't know if min.nc will improve the result or not and I don't have Amber16 compiled to try it out.
Tyler
Sent with [ProtonMail](
https://protonmail.com/) Secure Email.
------- Original Message -------
On Friday, February 18th, 2022 at 1:11 AM, ABDUL BASIT <abdul48_sit.jnu.ac.in> wrote:
> This is a problem in Amber16, it is working in amber 20.
>
> Yes, it is calcium loaded calmodulin structure (PDB ID 1CLL). I am trying to predict the calcium-binding site after removing calcium ions.
> I am using a placevent algorithm to place ions and compare their position from the ion in the PDB structure.
>
> Two of the calcium sites were predicted perfectly. Since calcium ions bind in a cooperative manner, I was trying to run 3D-RISM keeping those two ions as part of the solute.
>
> This is my third work on calmodulin.
>
> On Thu, Feb 17, 2022 at 1:22 AM tluchko <tluchko.protonmail.com> wrote:
>
>> Hi Abdul,
>>
>> I ran with your command
>>
>> rism3d.snglpnt --pdb rec.pdb --prmtop input.top --traj min.rst --closure kh --guv pdb --xvv SPCE_CaCl.xvv --buffer 30 --progress --verbose 2
>>
>> and I do not see see the distributions you sent. In the figure below, calcium ions are pink and the calcium (red), oxygen (blue) and chloride (green) distributions are shown at g(r)>8 isosurfaces.[vmdscene.jpg]
>>
>> I also tried looking at g(r) > 25 and only see distributions at two other coordinating sites. If I were to guess, I'd say that this protein looks like calmodulin and the two densities observed at g(r) > 25 correspond to the other two calcium binding sites on calmodulin.
>>
>> Is it possible that there were no calcium ions in the structure you provide 3D-RISM?
>>
>> Tyler
>>
>> Sent with [ProtonMail](https://protonmail.com/) Secure Email.
>>
>> ------- Original Message -------
>> On Tuesday, February 15th, 2022 at 8:58 PM, ABDUL BASIT <abdul48_sit.jnu.ac.in> wrote:
>>
>>> No problem, the required file is attached.
>>>
>>> On Wed, Feb 16, 2022 at 1:43 AM tluchko <tluchko.protonmail.com> wrote:
>>>
>>>> Sorry Abdul,
>>>>
>>>> Your email was flagged by my spam filter and I didn't see it until just now. I need your SPCE_CaCl.xvv. You sent the gvv file.
>>>>
>>>> Tyler
>>>>
>>>> Sent with [ProtonMail](https://protonmail.com/) Secure Email.
>>>>
>>>> ------- Original Message -------
>>>> On Thursday, February 10th, 2022 at 8:50 PM, ABDUL BASIT <abdul48_sit.jnu.ac.in> wrote:
>>>>
>>>>> Required files are attached.
>>>>>
>>>>> On Fri, Feb 11, 2022 at 5:26 AM tluchko <tluchko.protonmail.com> wrote:
>>>>>
>>>>>> Abdul,
>>>>>>
>>>>>> Can you provide input.top, min.rst and SPCE_CaCl.xvv?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Tyler
>>>>>>
>>>>>> Sent with ProtonMail Secure Email.
>>>>>>
>>>>>> ------- Original Message -------
>>>>>>
>>>>>> On Thursday, February 10th, 2022 at 10:00 AM, ABDUL BASIT <abdul48_sit.jnu.ac.in> wrote:
>>>>>>
>>>>>>> rism3d.snglpnt --pdb rec.pdb --prmtop input.top --traj min.rst --closure
>>>>>>>
>>>>>>> kh --guv pdb --xvv SPCE_CaCl.xvv --buffer 30
>>>>>>>
>>>>>>> On Thu, Feb 10, 2022 at 11:28 PM David A Case david.case.rutgers.edu
>>>>>>>
>>>>>>> wrote:
>>>>>>>
>>>>>>> > On Thu, Feb 10, 2022, ABDUL BASIT wrote:
>>>>>>> >
>>>>>>> > > for g(r)>25, there is a high probability of calcium ions at the position
>>>>>>> > >
>>>>>>> > > where calcium is already present as a part of solute as shown in the
>>>>>>> > >
>>>>>>> > > attached figure.
>>>>>>> >
>>>>>>> > Can you say exactly what commands you are using to do the rism3d
>>>>>>> >
>>>>>>> > calculation?
>>>>>>> >
>>>>>>> > ....dac
>>>>>>> >
>>>>>>> > AMBER mailing list
>>>>>>> >
>>>>>>> > AMBER.ambermd.org
>>>>>>> >
>>>>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>> AMBER mailing list
>>>>>>>
>>>>>>> AMBER.ambermd.org
>>>>>>>
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 18 2022 - 08:30:02 PST
