AMBER Archive (2005)

Subject: AMBER: tRNA's modified bases in the Amber parameters database

From: Whitney Allen (whitneygallen_at_yahoo.com)
Date: Mon Nov 07 2005 - 08:52:45 CST

Dear users,

I was trying to use the Case and Meyer's lib and frcmod files for the modified bases of tRNA-Phe which I found on the Amber Parameters Database (http://pharmacy.man.ac.uk/amber/). I tried loading them into the Amber 8 xleap module with the 6tna.pdb structure to see if I could get out prmtop and inpcrd files. Unfortunately I got some unrecognized atoms and a few fatal errors. Here are the commands and errors. Note that I saved the FRCMOD file as tRNA.frcmod and the OFF file as tRNA.lib.

 

% xleap –f leaprc.rna.ff99

 

Welcome to LEaP!

(no leaprc in search path)

Sourcing: /usr/local/fbscapp/amber8/dat/leap/cmd/leaprc.rna.ff99

Log file: ./leap.log

Loading parameters: /usr/local/fbscapp/amber8/dat/leap/parm/parm99.dat

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/all_nucleic94.lib

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/all_amino94.lib

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/all_aminoct94.lib

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/all_aminont94.lib

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/ions94.lib

Loading library: /usr/local/fbscapp/amber8/dat/leap/lib/solvents.lib

> loadamberparams tRNA.frcmod

Loading parameters: ./tRNA.frcmod

Reading force field mod type file (frcmod)

> loadoff tRNA.lib

Loading library: ./tRNA.lib

Bond: Maximum coordination exceeded on A<H5T 36>

-- setting atoms pert=true overrides default limits

> mol=loadpdb 6tna.pdb

Loading PDB file: ./6tna.pdb

Unknown residue: MO5 number: 76 type: Terminal/beginning

..relaxing end constraints to try for a dbase match

-no luck

Unknown residue: MO4 number: 77 type: Nonterminal

Unknown residue: MO6 number: 78 type: Nonterminal

Unknown residue: MO5 number: 79 type: Nonterminal

Created a new atom named: OXT within residue: .R<RG5 1>

Created a new atom named: P within residue: .R<RG5 1>

Created a new atom named: O1P within residue: .R<RG5 1>

Created a new atom named: O2P within residue: .R<RG5 1>

Created a new atom named: C2A within residue: .R<2MG 10>

Added missing heavy atom: .R<2MG 10>.A<CM2 19>

Created a new atom named: C2A within residue: .R<M2G 26>

Created a new atom named: C2B within residue: .R<M2G 26>

Added missing heavy atom: .R<M2G 26>.A<CM1 18>

Added missing heavy atom: .R<M2G 26>.A<CM2 22>

Created a new atom named: C2A within residue: .R<OMC 32>

Added missing heavy atom: .R<OMC 32>.A<CM2 16>

Created a new atom named: C2A within residue: .R<OMG 34>

Added missing heavy atom: .R<OMG 34>.A<CM2 16>

Created a new atom named: C5A within residue: .R<5MC 40>

Added missing heavy atom: .R<5MC 40>.A<CM5 14>

Created a new atom named: C7 within residue: .R<7MG 46>

Added missing heavy atom: .R<7MG 46>.A<CM7 20>

Created a new atom named: C5A within residue: .R<5MC 49>

Added missing heavy atom: .R<5MC 49>.A<CM5 14>

Created a new atom named: C5A within residue: .R<5MU 54>

Added missing heavy atom: .R<5MU 54>.A<C5M 13>

Created a new atom named: C1 within residue: .R<1MA 58>

Added missing heavy atom: .R<1MA 58>.A<CM1 20>

Creating new UNIT for residue: MO5 sequence: 77

Created a new atom named: MG within residue: .R<MO5 77>

Created a new atom named: OA within residue: .R<MO5 77>

Created a new atom named: OB within residue: .R<MO5 77>

Created a new atom named: OC within residue: .R<MO5 77>

Created a new atom named: OD within residue: .R<MO5 77>

Created a new atom named: OE within residue: .R<MO5 77>

Creating new UNIT for residue: MO4 sequence: 78

Created a new atom named: MG within residue: .R<MO4 78>

Created a new atom named: OB within residue: .R<MO4 78>

Created a new atom named: OC within residue: .R<MO4 78>

Created a new atom named: OD within residue: .R<MO4 78>

Created a new atom named: OF within residue: .R<MO4 78>

Creating new UNIT for residue: MO6 sequence: 79

Created a new atom named: MG within residue: .R<MO6 79>

Created a new atom named: OA within residue: .R<MO6 79>

Created a new atom named: OB within residue: .R<MO6 79>

Created a new atom named: OC within residue: .R<MO6 79>

Created a new atom named: OD within residue: .R<MO6 79>

Created a new atom named: OE within residue: .R<MO6 79>

Created a new atom named: OF within residue: .R<MO6 79>

Creating new UNIT for residue: MO5 sequence: 80

Created a new atom named: MG within residue: .R<MO5 80>

Created a new atom named: OA within residue: .R<MO5 80>

Created a new atom named: OB within residue: .R<MO5 80>

Created a new atom named: OC within residue: .R<MO5 80>

Created a new atom named: OD within residue: .R<MO5 80>

Created a new atom named: OE within residue: .R<MO5 80>

total atoms in file: 1740

Leap added 999 missing atoms according to residue templates:

10 Heavy

989 H / lone pairs

The file contained 38 atoms not in residue templates

> saveamberparm mol tRNA.prmtop tRNA.inpcrd

Checking Unit.

WARNING: The unperturbed charge of the unit: -74.004700 is not zero.

FATAL: Atom .R<RG5 1>.A<OXT 33> does not have a type.

FATAL: Atom .R<RG5 1>.A<P 34> does not have a type.

FATAL: Atom .R<RG5 1>.A<O1P 35> does not have a type.

FATAL: Atom .R<RG5 1>.A<O2P 36> does not have a type.

FATAL: Atom .R<2MG 10>.A<C2A 42> does not have a type.

FATAL: Atom .R<M2G 26>.A<C2A 45> does not have a type.

FATAL: Atom .R<M2G 26>.A<C2B 46> does not have a type.

FATAL: Atom .R<OMC 32>.A<C2A 35> does not have a type.

FATAL: Atom .R<OMG 34>.A<C2A 38> does not have a type.

FATAL: Atom .R<5MC 40>.A<C5A 39> does not have a type.

FATAL: Atom .R<7MG 46>.A<C7 46> does not have a type.

FATAL: Atom .R<5MC 49>.A<C5A 39> does not have a type.

FATAL: Atom .R<5MU 54>.A<C5A 38> does not have a type.

FATAL: Atom .R<1MA 58>.A<C1 47> does not have a type.

FATAL: Atom .R<MO5 77>.A<MG 1> does not have a type.

FATAL: Atom .R<MO5 77>.A<OA 2> does not have a type.

FATAL: Atom .R<MO5 77>.A<OB 3> does not have a type.

FATAL: Atom .R<MO5 77>.A<OC 4> does not have a type.

FATAL: Atom .R<MO5 77>.A<OD 5> does not have a type.

FATAL: Atom .R<MO5 77>.A<OE 6> does not have a type.

FATAL: Atom .R<MO4 78>.A<MG 1> does not have a type.

FATAL: Atom .R<MO4 78>.A<OB 2> does not have a type.

FATAL: Atom .R<MO4 78>.A<OC 3> does not have a type.

FATAL: Atom .R<MO4 78>.A<OD 4> does not have a type.

FATAL: Atom .R<MO4 78>.A<OF 5> does not have a type.

FATAL: Atom .R<MO6 79>.A<MG 1> does not have a type.

FATAL: Atom .R<MO6 79>.A<OA 2> does not have a type.

FATAL: Atom .R<MO6 79>.A<OB 3> does not have a type.

FATAL: Atom .R<MO6 79>.A<OC 4> does not have a type.

FATAL: Atom .R<MO6 79>.A<OD 5> does not have a type.

FATAL: Atom .R<MO6 79>.A<OE 6> does not have a type.

FATAL: Atom .R<MO6 79>.A<OF 7> does not have a type.

FATAL: Atom .R<MO5 80>.A<MG 1> does not have a type.

FATAL: Atom .R<MO5 80>.A<OA 2> does not have a type.

FATAL: Atom .R<MO5 80>.A<OB 3> does not have a type.

FATAL: Atom .R<MO5 80>.A<OC 4> does not have a type.

FATAL: Atom .R<MO5 80>.A<OD 5> does not have a type.

FATAL: Atom .R<MO5 80>.A<OE 6> does not have a type.

Failed to generate parameters

 

What can I do to get this to work for this tRNA-Phe? I would appreciate any help you might be able to give me. Thanks in advance.

Whitney Hastings

                
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