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.
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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
Created a new atom named: C1 within residue: .R<UNK 0>
Created a new atom named: C2 within residue: .R<UNK 0>
Created a new atom named: N3 within residue: .R<UNK 0>
Created a new atom named: N4 within residue: .R<UNK 0>
Created a new atom named: C5 within residue: .R<UNK 0>
Created a new atom named: C6 within residue: .R<UNK 0>
Created a new atom named: C7 within residue: .R<UNK 0>
---------
Created a new atom named: C19 within residue: .R<UNK 0>
Created a new atom named: C20 within residue: .R<UNK 0>
Created a new atom named: C21 within residue: .R<UNK 0>
Created a new atom named: C22 within residue: .R<UNK 0>
Created a new atom named: C23 within residue: .R<UNK 0>
Created a new atom named: C24 within residue: .R<UNK 0>
Created a new atom named: C25 within residue: .R<UNK 0>
total atoms in file: 25
The file contained 25 atoms not in residue templates
> saveamberparm t mol.top mol.crd
Checking Unit.
FATAL: Atom .R<UNK 0>.A<C1 1> does not have a type.
FATAL: Atom .R<UNK 0>.A<C2 2> does not have a type.
FATAL: Atom .R<UNK 0>.A<N3 3> does not have a type.
FATAL: Atom .R<UNK 0>.A<N4 4> does not have a type.
FATAL: Atom .R<UNK 0>.A<C5 5> does not have a type.
FATAL: Atom .R<UNK 0>.A<C6 6> does not have a type.
FATAL: Atom .R<UNK 0>.A<C7 7> does not have a type.
FATAL: Atom .R<UNK 0>.A<C8 8> does not have a type.
FATAL: Atom .R<UNK 0>.A<O9 9> does not have a type.
REJWAN ALI
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Received on Mon Jun 24 2013 - 14:30:03 PDT
