On Mon, Jun 24, 2013 at 5:25 PM, Rejwan <rejwan_88.yahoo.com> wrote:
> Hi
>
> Even though I loaded gaff FF and all needed PREPIN and FRCMOD, while
> trying generate TOP and CRD files using TLEAP I'm getting fatal error.
> Looking at the PREP file it seems all atoms in ligand are there with GAFF
> defination in PREP. Should I define the residue to get the atoms
> recognized by TLEAP ? It, however, worked without problem for another
> complex with same protein PDB. Thanks.
>
> _______________________________
>
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.gaff
> ----- Source: /packages/amber/12n/src/amber12/dat/leap/cmd/leaprc.gaff
> ----- Source of /packages/amber/12n/src/amber12/dat/leap/cmd/leaprc.gaff
> done
> Log file: ./leap.log
> Loading parameters: /packages/amber/12n/src/amber12/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> add. info. at the end
> > loadamberprep ./437.prep
> Loading Prep file: ./437.prep
> > loadamberparams ./437.frcmod
> Loading parameters: ./437.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> > t = loadpdb 437.pdb
> Loading PDB file: ./437.pdb
> Unknown residue: UNK number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: UNK sequence: 0
>
Look at the residue defined in 437.prep. The residue name in the PDB you
loaded is UNK. If the residue name is not UNK in the prep file, then that
is a problem. Make sure that the PDB and the prep file have the same name
for the same residue. Only then can leap appropriately map the atom types
(and parameters) from the residue template and parameter database to the
molecule in your PDB file.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 24 2013 - 15:00:02 PDT
