Hello:
I am building protein/ligand system in amber. Here is the last step
when I save the system:
> saveamberparm mol sys-gaff.prmtop sys-gaff.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1009 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
LIG 1
WAT 10824
)
(no restraints)
As we can see from the log file that it is said "no restraints". What
does it mean? Does it mean that the H-bond wasn't restrained with mshake
or something else?
I found found similar case from here:
http://archive.ambermd.org/201012/0246.html
However, the above talk was importing Gromacs system into Amber, but I
build a new system in Amber. My system have: protein, ligand and crystal
waters. I build the ligand parameters through acpype.py script. and here
is what I did for building system:
source leaprc.gaff
loadAmberParams frcmod.ionsjc_tip3p
loadamberparams ligand-gaff.frcmod
loadoff ligand-gaff.lib
mol = loadpdb input.pdb
solvatebox mol TIP3PBOX 10.6
charge mol
addions mol Na+ 11
charge mol
thank you very much
best
Albert
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Received on Mon Mar 18 2013 - 07:00:03 PDT
