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.
We are getting the same distribution as obtained for calcium-free protein.
The calcium ion is green when it is part of the solute and distribution
from 3D-RISM is shown in red color.
On Mon, Feb 7, 2022 at 10:37 AM ABDUL BASIT <abdul48_sit.jnu.ac.in> 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.
>
> We are getting the same distribution as obtained for calcium-free protein.
>
> The calcium ion is green when it is part of the solute and distribution
> from 3D-RISM is shown in red color.
>
> On Sat, Feb 5, 2022 at 10:39 PM Rakesh Srivastava <allahabad.21.gmail.com>
> wrote:
>
>> Thanks Dac. Your suggestion worked perfectly.
>>
>> On Thu, 3 Feb 2022 at 11:31 PM, David A Case <david.case.rutgers.edu>
>> wrote:
>>
>> > On Thu, Feb 03, 2022, Rakesh Srivastava wrote:
>> >
>> > >When I run 3drism calculation it gives following error:
>> > >addstrand: strand A already in mol
>> >
>> > First, can you say exactly what you did to "run 3drism calculation"?
>> >
>> > The "strand ID" is the same as what is usually called the "chain ID" in
>> PDB
>> > parlance. I'm guessing(!) that you are using a PDB file that has uses
>> the
>> > same chainID ("A") for different chains (aka strands). If so, you just
>> > need
>> > to make your chainID's unique. (ChainIDs are in column 22 in a PDB
>> file,
>> > and a new chain is initiated when a new ChainID is found, or when a TER
>> > card
>> > is encountered.)
>> >
>> > If my guess is wrong, we need more information: what commands you used,
>> > and any input PDB files that might be input.
>> >
>> > ...thx...dac
>> >
>> >
>> > _______________________________________________
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>> >
>> --
>> *Rakesh Srivastava*
>> Postdoctoral Fellow
>> Center for Computational Natural Sciences and Bioinformatics (CCNSB)
>> International Institute of Information Technology, Hyderabad
>> India
>> _______________________________________________
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>>
>
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Received on Wed Feb 09 2022 - 21:00:02 PST
