Well, concerning the first question, whis kind of error appears typically
when you try to copy a non-existent unit/atom/etc. to create a new thing.
use the list command to make sure ADE really _is_ an existing residue in
your session. If not, you have to import it (it is not part of the
standard stuff, ie. it is not loaded with the default leaprc script, at
least not in the standard AMBER6 dist.).
for eg. R=copy ALA would go, since there is an ALA named residue
predefined. Look into all-amino94.in for amino acid residue
names (this file is in the dat subdir. of the amber package).
If you modify the pdb file, and change a residue name there, it is a good
idea to create the new residue in leap _before_ you load the pdb, this way
when importing the pdb-file, leap would automatically recognise the new
residue. Parameters (charge, etc.) can also be changed later with the edit
command. (but then be sure to edit the residue in the protein, not the
template..). If you make up the new residue knowing all of its parameters
in the particular case, creating the residue with these params, will give
the advantage that this will be automatically assigned to the residue in
the protein when you read the pdb.
As of the charge, if i'm not mistaken, no scale factor is used.
hope this helps,
good luck,
Gusztav.
-----------------------
Gusztav SCHAY
PhD student
Semmelweis University Budapest
Dept. of Biophysics and Radiation Biology
Budapest
Puskin u. 9.
H-1088
Hungary
phone: +36-1-2662755 #4033
fax: +36-1-2666656
email: schayg_at_puskin-a206.sote.hu
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Received on Wed Oct 04 2000 - 11:12:33 PDT
