Please explain why you think it should be different. People need more
information to help than you have been providing.
On Fri, Aug 9, 2024, 12:21 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> 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 Fri Aug 09 2024 - 04:00:02 PDT
