Dear Urszula,
> I was wondering, how did you prepare the ACE-LYA.pdb file in xleap?
> when I load it by typing x = loadpdb ACE-LYA.pdb I get list of
> different errors...
xLEaP is buggy in some conditions, but it is also very powerful. Once
you know how to use it, you can potentially built all the structures
you need; I mean with LEaP & its graphical interface xLEaP this is
very easy to build new structures from scratch.
There is this 'relax' option;
see also
http://q4md-forcefieldtools.org/Tutorial/leap.php for its
implementation in tLEaP to relax any bad input geometry (try doing it
with defined atom types and without any atom type defined).
The best bet to get good input structure for a QM job is to (i) load
an Amber force field (ii) edit a new empty unit (iii) create the
structure using Select/Twist/Move/Erase/Draw (iv) add the hydrogens
and build (v) delete unwanted hydrogens (many unwanted hydrogens are
often added) (vi) add the atom types for the group of atoms to be
relaxed (if one does not like the geometry of a part of the molecule)
and (vii) relax the selected group, etc...
xleap -f leaprc.ff99SB
# create an empty unit TOTO
edit TOTO
# Click on/Activate "Draw" by selecting the carbon atom
# Draw a bad structure
# Make it more presentable:
# "Unit/Add H & Build"
# Select another atom and redo the same procedure
# Select a group of atoms with the mouse left button
# "Edit/Selected atom" to add the atom type (and modify atom names)
# Provide the atom types in the table for the group of atom selected
# Save and quit the table
# "Table/Save and quit"
# Edit/Relax selection...
then you save TOTO into the PDB file format and you can use your
favorite text editor to modify the atom order, modify atom and residue
names, etc...
then you can reload TOTO in LEaP
TOTO = loadpdb TOTO.pdb
bondbydistance
# and create a new structure from TOTO etc...
etc...
You can use R.E.D. Server as well; see:
http://q4md-forcefieldtools.org/REDS/faq.php#18
http://q4md-forcefieldtools.org/REDS/faq.php#19
http://q4md-forcefieldtools.org/REDS/faq.php#20
regards, Francois
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Received on Mon Nov 07 2011 - 06:30:04 PST
