Ok. So I'm using this ff because of a paper I read and wanted to do some
analysis using the same ff, but if you have a better one for protein-rna
that it is even better!
So I've attached the starting PDB file and here the commands with the
output (avoid addions and solvatebox)
* $AMBERHOME/bin/tleap -s -f
/home/mgatti/Scrivania/amber14//dat/leap/cmd/oldff/leaprc.ff99SB*
-I: Adding /home/mgatti/Scrivania/amber14//dat/leap/prep to search path.
-I: Adding /home/mgatti/Scrivania/amber14//dat/leap/lib to search path.
-I: Adding /home/mgatti/Scrivania/amber14//dat/leap/parm to search path.
-I: Adding /home/mgatti/Scrivania/amber14//dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /home/mgatti/Scrivania/amber14//dat/leap/cmd/oldff/leaprc.ff99SB.
Welcome to LEaP!
Sourcing: /home/mgatti/Scrivania/amber14//dat/leap/cmd/oldff/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /home/mgatti/Scrivania/amber14//dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/home/mgatti/Scrivania/amber14//dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/home/mgatti/Scrivania/amber14//dat/leap/lib/all_nucleic94.lib
Loading library:
/home/mgatti/Scrivania/amber14//dat/leap/lib/all_amino94.lib
Loading library:
/home/mgatti/Scrivania/amber14//dat/leap/lib/all_aminoct94.lib
Loading library:
/home/mgatti/Scrivania/amber14//dat/leap/lib/all_aminont94.lib
Loading library: /home/mgatti/Scrivania/amber14//dat/leap/lib/ions94.lib
Loading library: /home/mgatti/Scrivania/amber14//dat/leap/lib/solvents.lib
*mol = loadPdb chain_B_D.pdb*
Loading PDB file: ./chain_B_D.pdb
Created a new atom named: P within residue: .R<RU5 13>
Created a new atom named: OP1 within residue: .R<RU5 13>
Created a new atom named: OP2 within residue: .R<RU5 13>
Added missing heavy atom: .R<CTYR 360>.A<OXT 22>
total atoms in file: 3007
Leap added 3039 missing atoms according to residue templates:
1 Heavy
3038 H / lone pairs
The file contained 3 atoms not in residue templates
> *check mol *
Checking 'mol'....
WARNING: The unperturbed charge of the unit: -4.000000 is not zero.
FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.
FATAL: Atom .R<RU5 13>.A<OP1 30> does not have a type.
FATAL: Atom .R<RU5 13>.A<OP2 31> does not have a type.
Warning: Close contact of 0.719811 angstroms between .R<RU5 13>.A<H5T 1>
and .R<RU5 13>.A<P 29>
Warning: Close contact of 1.451155 angstroms between .R<RA 16>.A<H2'1 30>
and .R<RU 17>.A<H5'2 7>
Warning: Close contact of 1.470423 angstroms between .R<ARG 23>.A<HE 15>
and .R<ARG 23>.A<HA 4>
Warning: Close contact of 1.429631 angstroms between .R<GLN 37>.A<HG3 10>
and .R<GLU 40>.A<HG3 10>
Warning: Close contact of 1.185349 angstroms between .R<GLN 71>.A<HE22 15>
and .R<ASN 75>.A<HD21 11>
Warning: Close contact of 1.495973 angstroms between .R<ALA 80>.A<H 2> and
.R<WAT 365>.A<H2 3>
Warning: Close contact of 1.499931 angstroms between .R<LYS 155>.A<HZ1 18>
and .R<WAT 438>.A<H1 2>
Warning: Close contact of 1.452440 angstroms between .R<ILE 182>.A<HD12 16>
and .R<CYS 209>.A<HG 9>
Warning: Close contact of 1.356054 angstroms between .R<ARG 200>.A<HE 15>
and .R<ARG 200>.A<HA 4>
Warning: Close contact of 1.414351 angstroms between .R<LEU 215>.A<HB3 7>
and .R<PRO 216>.A<HD3 4>
Warning: Close contact of 1.439079 angstroms between .R<HIE 222>.A<HE2 13>
and .R<ASP 249>.A<OD1 9>
Warning: Close contact of 1.377523 angstroms between .R<GLU 243>.A<HG2 9>
and .R<HIE 280>.A<HE2 13>
Warning: Close contact of 1.064759 angstroms between .R<ILE 257>.A<HG13 13>
and .R<CYS 277>.A<HG 9>
Warning: Close contact of 0.957682 angstroms between .R<LEU 262>.A<H 2> and
.R<WAT 362>.A<H1 2>
Warning: Close contact of 1.121643 angstroms between .R<VAL 263>.A<H 2> and
.R<WAT 376>.A<H1 2>
Warning: Close contact of 1.410025 angstroms between .R<SER 265>.A<HG 9>
and .R<MET 307>.A<HE1 13>
Warning: Close contact of 1.497795 angstroms between .R<VAL 293>.A<HG13 10>
and .R<LEU 304>.A<HG 9>
Warning: Close contact of 0.880653 angstroms between .R<HIE 339>.A<HE2 13>
and .R<WAT 415>.A<H1 2>
Warning: Close contact of 1.408692 angstroms between .R<THR 342>.A<HG23 10>
and .R<TYR 346>.A<HE2 17>
Warning: Close contact of 1.448872 angstroms between .R<WAT 372>.A<H1 2>
and .R<WAT 389>.A<H2 3>
Warning: Close contact of 1.254887 angstroms between .R<WAT 394>.A<H1 2>
and .R<WAT 423>.A<H2 3>
Checking parameters for unit 'mol'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 3 Warnings: 22
> *saveamberparm mol test_amber.prmtop test_amber.inpcrd*
Checking Unit.
WARNING: The unperturbed charge of the unit: -4.000000 is not zero.
FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.
FATAL: Atom .R<RU5 13>.A<OP1 30> does not have a type.
FATAL: Atom .R<RU5 13>.A<OP2 31> does not have a type.
Failed to generate parameters
Parameter file was not saved.
2015-01-29 13:50 GMT+01:00 David A Case <case.biomaps.rutgers.edu>:
> On Thu, Jan 29, 2015, Mahad Gatti Iou wrote:
> >
> > Created a new atom named: OP1 within residue: .R<RU5 1>
> > Created a new atom named: OP2 within residue: .R<RU5 1>
>
> This means that your PDB file has an atom named OP1 in residue 1, but no
> such
> atom exists in the residue library.
>
> You have to make sure that the pdb file and residue library match. Since
> we
> don't know where your PDB file came from, we cannot be of much help. In
> particular, it's hard to see how/why you would get this message for OP1 and
> OP2, but not for P.
>
> The fact that you are using a obsolete residue name (RU) instead of the
> current standard (U) arises from the fact that you are loading a 20-year
> old
> library file. Updating is highly recommended, but it won't solve the
> problem
> listed above.
>
> ....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 Thu Jan 29 2015 - 05:30:02 PST
