On Sat, May 29, 2010, William Flak wrote:
> Dear AMBERI have still a problem with the extrapoint.In my LIG.mol2 I called the extrapoint as following: 16 EP -5.9720 0.4190 0.6080 EP 1 LIG -0.046045
> I fired up tleap and typed:source leaprc.gaffsource leaprc.ff02polEP.r1 set default PBRadii mbondi2LIG = loadmol2 LIG.mol2saveoff LIG LIG.libloadamberparams LIG.frcmodCOM = loadpdb COMbase.pdb
> it gives me the following error:Loading PDB file: ./1GXZbase.pdb total atoms in file: 4190 Leap added 565 missing atoms according to residue templates: 565 unknown element
> All of these unknown elements are returned to EP.How should I define EP?Some helpers told me ff92EP force field has defined EP element.So, what I missed?Any comment would be highly appreciated.Thanks in advance;W. Falk
(It would help if you could format you emails as plain text.)
The message above leads to more questions than it answers. You seem to be
typing "COM = loadpdb COMbase.pdb", but the error message refers to
./1GXZbase.pdb.
You state that the extra point is in the LIG.mol2 file. Why are there 565
extra points in the pdb file? What is in the pdb file anyway?
You will need to make a *minimal* test case that illustrates the error,
probably just the ligand by itself.
Generally, defining EP in a parm.dat file, and as a element in the
addAtomTypes array (usually found in the leaprc file) should be enought.
....dac
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Received on Sat May 29 2010 - 15:00:03 PDT
