Hi Armin,
You can just use the savepdb command in leap.
E.g.
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
loadoff mylib.lib
savepdb UNITNAME pdb_name.pdb
In xleap you can get a list of commands with the help command. Help on it's
own lists all the command while for example 'help savepdb' will give you
help on the savepdb command. You can also do things like saveamberprep which
will give you a prep file that I believe Antechamber can read.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of opitz.che.udel.edu
> Sent: 13 April 2005 14:37
> To: amber.scripps.edu
> Subject: AMBER: xleap, lib file question
>
> Dear Amber Community,
>
> I have a pdb file for a relatively small organic molecule. After
> importing it into xleap, I modify it by adding a few atoms within the
> unit editor.
> At this point I can save the *.lib file, but cannot save the
> *.prmtop and
> *.inpcrd file, because I haven't specified the atom types.
> This I don't
> want to do until after I have run the modified structure through
> antechamber (to get the atom types from the prepin file).
> Therefore, is there a way to get a pdb file from the *.lib file saved
> from xleap?
> Other suggestions of how to get around this would also be welcome.
>
> Best Regards,
>
> Armin
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 13 2005 - 23:53:00 PDT
