Dear Dr. Case,
I had not seen such non-consecutive atom numbers in pdb file format;
in standard file format, atom numbers look like consecutive; That's why I
was worried thinking it may affect my MD simulation. But, I found that such
non consecutive atom numbers did not make any difference in the molecular
dynamics simulation.
Thank you for help,
Mahendra Thapa
Ph.D Candidate ( Physics)
University of Cincinnati,OH
On Sun, Apr 15, 2012 at 9:26 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: case
> Sent: Sunday, April 15, 2012 8:25:57 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: reduce and trim function
>
> On Sun, Apr 15, 2012, Mahendra B Thapa wrote:
> >
> > The problem mentioned in
> > the previous mail only appeared when used reduce command.
>
> > > > Atom number of a pdb [ 2nd column ] is not
> continuous
> > > > after using trim and reduce of AMBER command , instead " new"
> appears in
> > > > the last column.
>
> I don't think I ever understood what the "problem" was, but maybe I am
> missing
> something. My recollection was that you were unhappy that the atom numbers
> were not consecutive, but I don't remember seeing any reason why that
> would be
> a problem; that is: why do you want (or need) consecutive atom numbers?
>
> ....dac
>
>
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>
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Received on Mon Apr 30 2012 - 15:30:04 PDT
