I figured it out... I didn't realize there was a connection between the
variable name (in tleap) and the name of the molecule in mol2 and the pdb
file. I had the mol2 and pdb the same (DIZ) but just used a generic name
(benz - see below). when i used DIZ instead of benz in tleap. everything
worked fine...
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Volumes/jonathan/amber12/dat/leap/cmd/leaprc.ff12SB
Log file: ./leap.log
Loading parameters: /Volumes/jonathan/amber12/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /Volumes/jonathan/amber12/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/amino12.lib
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/aminoct12.lib
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/aminont12.lib
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/nucleic12.lib
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/ions08.lib
Loading library: /Volumes/jonathan/amber12/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /Volumes/jonathan/amber12/dat/leap/cmd/leaprc.gaff
----- Source of /Volumes/jonathan/amber12/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /Volumes/jonathan/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
> benz=loadmol2 benz.mol2
Loading Mol2 file: ./benz.mol2
Reading MOLECULE named DIZ
> check benz
Checking 'benz'....
Checking parameters for unit 'benz'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> loadamberparams benz.frcmod
Loading parameters: ./benz.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff benz benz.lib
Building topology.
Building atom parameters.
> loadoff benz.lib
Loading library: ./benz.lib
> complex=loadpdb 1T4Ea.pdb
Loading PDB file: ./1T4Ea.pdb
Unknown residue: DIZ number: 96 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: DIZ sequence: 112
Created a new atom named: CL1 within residue: .R<DIZ 112>
Created a new atom named: C1 within residue: .R<DIZ 112>
Created a new atom named: C2 within residue: .R<DIZ 112>
Created a new atom named: C3 within residue: .R<DIZ 112>
Created a new atom named: C4 within residue: .R<DIZ 112>
Created a new atom named: C5 within residue: .R<DIZ 112>
Created a new atom named: C6 within residue: .R<DIZ 112>
Created a new atom named: C7 within residue: .R<DIZ 112>
Created a new atom named: C8 within residue: .R<DIZ 112>
Created a new atom named: O1 within residue: .R<DIZ 112>
Created a new atom named: O2 within residue: .R<DIZ 112>
Created a new atom named: N1 within residue: .R<DIZ 112>
Created a new atom named: C9 within residue: .R<DIZ 112>
Created a new atom named: O3 within residue: .R<DIZ 112>
Created a new atom named: C10 within residue: .R<DIZ 112>
Created a new atom named: C11 within residue: .R<DIZ 112>
Created a new atom named: C12 within residue: .R<DIZ 112>
Created a new atom named: I1 within residue: .R<DIZ 112>
Created a new atom named: C13 within residue: .R<DIZ 112>
Created a new atom named: C14 within residue: .R<DIZ 112>
Created a new atom named: C15 within residue: .R<DIZ 112>
Created a new atom named: N2 within residue: .R<DIZ 112>
Created a new atom named: C16 within residue: .R<DIZ 112>
Created a new atom named: O4 within residue: .R<DIZ 112>
Created a new atom named: C17 within residue: .R<DIZ 112>
Created a new atom named: C18 within residue: .R<DIZ 112>
Created a new atom named: C19 within residue: .R<DIZ 112>
Created a new atom named: C20 within residue: .R<DIZ 112>
Created a new atom named: C21 within residue: .R<DIZ 112>
Created a new atom named: CL2 within residue: .R<DIZ 112>
Created a new atom named: C22 within residue: .R<DIZ 112>
Created a new atom named: C23 within residue: .R<DIZ 112>
total atoms in file: 816
Leap added 816 missing atoms according to residue templates:
816 H / lone pairs
The file contained 32 atoms not in residue templates
> saveamberparm complex 1t4ea.prmtop 1t4ea.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 4.000000 is not zero.
FATAL: Atom .R<DIZ 112>.A<CL1 1> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C1 2> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C2 3> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C3 4> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C4 5> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C5 6> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C6 7> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C7 8> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C8 9> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O1 10> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O2 11> does not have a type.
FATAL: Atom .R<DIZ 112>.A<N1 12> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C9 13> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O3 14> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C10 15> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C11 16> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C12 17> does not have a type.
FATAL: Atom .R<DIZ 112>.A<I1 18> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C13 19> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C14 20> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C15 21> does not have a type.
FATAL: Atom .R<DIZ 112>.A<N2 22> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C16 23> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O4 24> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C17 25> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C18 26> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C19 27> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C20 28> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C21 29> does not have a type.
FATAL: Atom .R<DIZ 112>.A<CL2 30> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C22 31> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C23 32> does not have a type.
Failed to generate parameters
Parameter file was not saved.
>
On Fri, Dec 7, 2012 at 4:18 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Dec 07, 2012, Jonathan Gough wrote:
>
> > I am trying to load a complex into amber. I followed the directions as
> > posted previously.
> >
> > >From reading the mailing archives this is supposed to be caused by the
> > names in the .mol2 file not matching those in the PDB.
> >
> > I can't seem to see where there is a difference or why I am getting this
> > error... I used the same part of the PDB to create the mol2, from what I
> > can see I can't figure out what is wrong...
>
> We need to see the entire LEaP output. Did you load gaff.dat? Exactly how
> did you load the mol2 file? etc. Basically, we need to see the exact
> sequence of commands given to LEaP.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 07 2012 - 14:00:02 PST
