Please anyone respond
On Thu, 8 Aug 2024, 9:14 am Dulal Mondal, <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
> Dear Experts,
> I follow the manual of amber24 (chapter 28). In the parm file there is a
> portion "RAD". It carries 0 and 1 values. The definition of RAD is also
> given. ( Atoms which are going to disappear
> are identified with 1.0 in the deprotonated flags and 0.0 in the
> protonated flags. Atoms which are
> always present are identified as 0.0 in both sets of flags).
>
> But in the example of the parm file (phmdparm section, 610-613 pages) the
> values are given for HIP.
> RAD(3,:) = 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,
> 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
> 0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
> 0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,
>
> I think it should be like below.
> RAD(3,:) = 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
> 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
> 0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,
> 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
>
>
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
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Received on Thu Aug 08 2024 - 21:30:02 PDT
