Hi,
Thank you for your query. Actually I wanted to calculate different types of
interactions like ionic interactions, hydrophobic interactions, etc between
amino acids and ligand during simulation run. Just like the hbond command
of *cpptraj* which gives detailed information regarding hydrogen bond
numbers, acceptor, donors, frequency of bond formation, etc. So, I wanted
to know if there is any command like that for calculating ionic,
hydrophobic interactions and other forces.
Thank you
On Thu, Jun 20, 2024 at 11:52 AM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Hi Sayan,
>
> you should clarify what you mean by "most interacting", that is, what do
> you intend to calculate.
>
> Though I guess the ptraj hydrogen bonding routines may be helpful here?
>
> Kind Regards,
>
> Thomas
>
> On Wed, Jun 19, 2024 at 7:46 PM Sayan Poddar via AMBER <amber.ambermd.org>
> wrote:
>
>> **Warning** The sender address (Sayan Poddar via AMBER ) can not be
>> verified, sender email address could be spoofed. Please take care to
>> proceed.
>> Dear AMBER developers and Users,
>>
>> Is there any method of calculating the most interacting amino acid
>> residues of a simulated ligand protein complex in amber?
>>
>> Thank you
>>
>> --
>> *with regards*
>> *Sayan Poddar*
>>
>> *PhD Research Scholar*
>> *Department of Biosciences and Biomedical Engineering*
>> *Indian Institute of Technology Indore*
>> *India*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
--
*with regards*
*Sayan Poddar*
*PhD Research Scholar*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology Indore*
*India*
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Received on Thu Jun 20 2024 - 03:00:02 PDT
