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
Received on Wed Jan 18 2012 - 10:30:03 PST
