Hi Sebastian,
> If this is the case then shouldn't the only change I need to make be in
> tleap02.in :
> -----------------------------------
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberparams ligand_addH_antechamber.frcmod
> loadoff ptb.lib
> complex = loadpdb COMPLEX.PDB ************************ #old line was
> `complex = loadpdb receptor.pdb`
> addions complex Na+ 10
> solvatebox complex TIP3PBOX 8.0
> saveamberparm complex initial_complex.prm7 initial_complex.rst7
> savepdb complex initial_complex.pdb
> ------------------------------------
yes, that should be enough. the loadoff command defines a PTB residue for
leap, then when it encounters one in your complex.pdb, it will use the
parameters you made for it, assigning atoms types, charges and even adding
missing atoms (like hydrogens). Where info exists in the pdb (e.g. heavy
atom coordinates) it is used over that in your unit definition. The only
requirement is that your lib file needs to have the same atom and residue
names as the pdb.
Alternatively, you could loadoff the PTB unit and loadpdb your receptor
and then do
COMPLEX = combine { RECEPTOR PTB }
but you would have to be careful that the relative orientation of the
molecules hasnt changed, since programs like to e.g. place centers of mass
into the origin automatically.
In my opinion, the second approach has no apparent benefit, but feel free
to try which suits your workflow better
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Apr 11 2013 - 02:30:02 PDT
