You really need to provide all commands you have used in leap to be
able to get to the bottom of this. Also, if possible, provide the
original input file(s). Essentially, anybody trying to reproduce your
error should be able to run this for themselves.
Is there any particular reason why it must be the old ff99SB forcefield?
On Thu, 29 Jan 2015 10:50:41 +0100
Mahad Gatti Iou <mahaddino.gmail.com> wrote:
> first of all thanks for the info!
>
> I'm gonna try to be as much simple as i can.
> So all the RU stuff where it is possible to read? 'Cos in the Amber
> User Guide I don't think it is explained.
> Second, I looked up the /leap/lib/all_nucleic94.lib but still didn't
> get the solution of the problem.
>
> I want to simulate a protein-RNA complex using Amber ff99SB force
> field and NAMD software. Since the PSF file is not possible to obtain
> (apparently) usign the amber parm99.dat file, I have to use leap to
> obtain the starting files and then use NAMD.
> Using the check command the output is this:
>
> mol =loadpdb pdb4amber.pdb
> Loading PDB file: ./pdb4amber.pdb
> Created a new atom named: OP1 within residue: .R<RU5 1>
> Created a new atom named: OP2 within residue: .R<RU5 1>
> Added missing heavy atom: .R<CTYR 348>.A<OXT 22>
> total atoms in file: 3006
> Leap added 3039 missing atoms according to residue templates:
> 1 Heavy
> 3038 H / lone pairs
> The file contained 2 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 1>.A<OP1 29> does not have a type.
> FATAL: Atom .R<RU5 1>.A<OP2 30> does not have a type.
> Warning: Close contact of 1.451155 angstroms between .R<RA 4>.A<H2'1
> 30> and .R<RU 5>.A<H5'2 7>
> Warning: Close contact of 1.470423 angstroms between .R<ARG 11>.A<HE
> 15> and .R<ARG 11>.A<HA 4>
> Warning: Close contact of 1.429631 angstroms between .R<GLN 25>.A<HG3
> 10> and .R<GLU 28>.A<HG3 10>
> Warning: Close contact of 1.185349 angstroms between .R<GLN
> 59>.A<HE22 15> and .R<ASN 63>.A<HD21 11>
> Warning: Close contact of 1.495973 angstroms between .R<ALA 68>.A<H
> 2> and .R<WAT 353>.A<H2 3>
> Warning: Close contact of 1.499931 angstroms between .R<LYS
> 143>.A<HZ1 18> and .R<WAT 426>.A<H1 2>
> Warning: Close contact of 1.452440 angstroms between .R<ILE
> 170>.A<HD12 16> and .R<CYS 197>.A<HG 9>
> Warning: Close contact of 1.356054 angstroms between .R<ARG 188>.A<HE
> 15> and .R<ARG 188>.A<HA 4>
> Warning: Close contact of 1.414351 angstroms between .R<LEU
> 203>.A<HB3 7> and .R<PRO 204>.A<HD3 4>
> Warning: Close contact of 1.439079 angstroms between .R<HIE
> 210>.A<HE2 13> and .R<ASP 237>.A<OD1 9>
> Warning: Close contact of 1.377523 angstroms between .R<GLU
> 231>.A<HG2 9> and .R<HIE 268>.A<HE2 13>
> Warning: Close contact of 1.064759 angstroms between .R<ILE
> 245>.A<HG13 13> and .R<CYS 265>.A<HG 9>
> Warning: Close contact of 0.957682 angstroms between .R<LEU 250>.A<H
> 2> and .R<WAT 350>.A<H1 2>
> Warning: Close contact of 1.121643 angstroms between .R<VAL 251>.A<H
> 2> and .R<WAT 364>.A<H1 2>
> Warning: Close contact of 1.410025 angstroms between .R<SER 253>.A<HG
> 9> and .R<MET 295>.A<HE1 13>
> Warning: Close contact of 1.497795 angstroms between .R<VAL
> 281>.A<HG13 10> and .R<LEU 292>.A<HG 9>
> Warning: Close contact of 0.880653 angstroms between .R<HIE
> 327>.A<HE2 13> and .R<WAT 403>.A<H1 2>
> Warning: Close contact of 1.408692 angstroms between .R<THR
> 330>.A<HG23 10> and .R<TYR 334>.A<HE2 17>
> Warning: Close contact of 1.448872 angstroms between .R<WAT 360>.A<H1
> 2> and .R<WAT 377>.A<H2 3>
> Warning: Close contact of 1.254887 angstroms between .R<WAT 382>.A<H1
> 2> and .R<WAT 411>.A<H2 3>
> Checking parameters for unit 'mol'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 2 Warnings: 21
>
>
>
> 2015-01-28 18:54 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
>
> > On Wed, 2015-01-28 at 18:01 +0100, Mahad Gatti Iou wrote:
> > > Hello everyone,
> > >
> > > I'm new to AMBER, so I was reading other emails about the same
> > > topic as well as the user guide to start learning a little bit
> > > more. Basically, I want to run a simulation with NAMD using AMBER
> > > force field. Apparently it is not possible to use VMD's PSFgen
> > > plugin to obtain the parameter file, so I'm learning how to do
> > > that through leap. So far so good, I'm following a tutorial as
> > > well. When I'm loading the molecule I found this error, I got
> > > that there's some problem around the names of the residues in the
> > > PDB file and how AMBER actually reads them but still I wasn't
> > > able to find any information about what RU5 (and in general the
> > > syntax) is.
> >
> > RU5 is the (old old old) residue name of a 5'-terminal ribouracil
> > residue. If that helps, great, but I suspect it doesn't.
> >
> > > Can I receive some help regarding this matter?
> >
> > Residue names in the PDB file *must* match the residue names in the
> > corresponding residue libraries (inside $AMBERHOME/dat/leap/lib).
> > These follow the PDB standard for the most part, but each protomer
> > or tautomer (e.g., protonated carboxylic acids, or epsilon- vs.
> > delta-protonated histidine) has a separate name which must be
> > changed in the PDB file to get the desired tautomer.
> >
> > I would also suggest trying the "pdb4amber" tool, which should help
> > prepare your PDB file for use with leap.
> >
> > For anything more than that, you will need to provide a lot more
> > details (with a lot more specificity) if you want help. Simplify
> > the problem as much as possible, then give exact input and output
> > rather than trying to describe it.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jan 29 2015 - 03:00:02 PST
