Re: [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.

From: Mahad Gatti Iou <>
Date: Thu, 29 Jan 2015 10:50:41 +0100

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 <>:

> 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
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Received on Thu Jan 29 2015 - 02:00:02 PST
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