On Wed, Jan 18, 2012 at 2:44 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
> Hi, Jason
>
I have used XLeaP , not tleap. I am trying to
reproduce the same as of tutorial.
Thank you for help,
Mahendra Thapa
>
>
> ________________________________________
> From: Jason Swails
> Sent: Wednesday, January 18, 2012 1:43:26 PM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL
> A1 - SECTION 1]
>
> 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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jan 18 2012 - 12:30:03 PST
