AMBER Archive (2005)

Subject: RE: AMBER: xleap, lib file question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 13 2005 - 17:07:04 CDT

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

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of opitz_at_che.udel.edu
> Sent: 13 April 2005 14:37
> To: amber_at_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
>
>
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