I don't think tleap prints CONECT records, since it doesn't need them
itself. It does, however, use TER cards (which is why those are present).
HTH,
Jason
On Wed, Jan 18, 2012 at 1:25 PM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> On Tue, Jan 17, 2012 at 9:15 PM, Thapa, Mahendra (thapamb) <
> thapamb.mail.uc.edu> wrote:
>
> >
> > Dear Dr. Case,
> >
>
> Yes, I got image with the command "edit 1PLC_mod"
>
> As suggested in previous posts in AMBER, I tried to save this as
> XLeap:Universal Editor ----> File
> ---------> SavePDB file--------->
> 1PLC_mod [ I put file this name ] ---------> accept
>
> Then, I got the file[ 1PLC_mod] in my folder but this is different from
> that the tutorial: in my file, there are TER card after each water molecule
> but no connectivities.
>
> Thank you for the help,
> Mahendra Thapa
>
>
> >
> > ________________________________________
> > From: case
> > Sent: Tuesday, January 17, 2012 8:14:10 PM (UTC-06:00) Central America
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1
> -
> > SECTION 1]
> >
> > On Tue, Jan 17, 2012, Mahendra B Thapa wrote:
> > >
> > > In AMBER11 XLEaP Universal Editor, I use the following
> command:
> > > 1PLC_mod = loadpdb "
> > 1PLC.pdb"
> > > At the end of the editor, I got the message as
> > > total atoms in
> file:1656
> > > Leap added 341 missing atoms according to residue templates:
> > > 341 H / lone pairs
> > > The file contained 122 atoms not in residue templates
> >
> > So far so good.
> >
> > > When I command edit 1PLC.pdb, XLeaP unit editor displayed nothing.
> >
> > The proper command is "edit 1PLC_mod": you edit the unit name, not the
> pdb
> > filename. Use the LIST command to display the units that are
> > loaded...those
> > are the things you can edit.
> >
> > [Arguably, xleap should give a better error message...]
> >
> > ...hope this helps...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 18 2012 - 12:00:02 PST
