Sorry about the duplicate message but here is are the steps I tried:
tleap
-I: Adding /usr/local/bio/amber20/dat/leap/prep to search path.
-I: Adding /usr/local/bio/amber20/dat/leap/lib to search path.
-I: Adding /usr/local/bio/amber20/dat/leap/parm to search path.
-I: Adding /usr/local/bio/amber20/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.RNA.OL3
----- Source: /usr/local/bio/amber20/dat/leap/cmd/leaprc.RNA.OL3
----- Source of /usr/local/bio/amber20/dat/leap/cmd/leaprc.RNA.OL3 done
Log file: ./leap.log
Loading parameters: /usr/local/bio/amber20/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading library: /usr/local/bio/amber20/dat/leap/lib/RNA.lib
> list
A A3 A5 AN C C3 C5 CN
G G3 G5 GN OHE U U3 U5
UN parm10
> source leaprc.water.opc
----- Source: /usr/local/bio/amber20/dat/leap/cmd/leaprc.water.opc
----- Source of /usr/local/bio/amber20/dat/leap/cmd/leaprc.water.opc done
Loading library: /usr/local/bio/amber20/dat/leap/lib/atomic_ions.lib
Loading library: /usr/local/bio/amber20/dat/leap/lib/solvents.lib
Loading parameters: /usr/local/bio/amber20/dat/leap/parm/frcmod.opc
Reading force field modification type file (frcmod)
Reading title:
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871)
Loading parameters:
/usr/local/bio/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung &
Cheatham JPCB (2008)
Loading parameters:
/usr/local/bio/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water
model (12-6 normal usage set)
> rna = loadpdb file.edited.pdb
Loading PDB file: ./file.edited.pdb
Created a new atom named: P within residue: .R<C5 1>
Created a new atom named: OP1 within residue: .R<C5 1>
Created a new atom named: OP2 within residue: .R<C5 1>
Added missing heavy atom: .R<A 55>.A<O2' 31>
Added missing heavy atom: .R<A 55>.A<N9 13>
Added missing heavy atom: .R<A 55>.A<C8 14>
Added missing heavy atom: .R<A 55>.A<C4 26>
Added missing heavy atom: .R<A 55>.A<N7 16>
Added missing heavy atom: .R<A 55>.A<C5 17>
Added missing heavy atom: .R<A 55>.A<N3 25>
Added missing heavy atom: .R<A 55>.A<C6 18>
Added missing heavy atom: .R<A 55>.A<C2 23>
Added missing heavy atom: .R<A 55>.A<N6 19>
Added missing heavy atom: .R<A 55>.A<N1 22>
total atoms in file: 2138
Leap added 19 missing atoms according to residue templates:
11 Heavy
8 H / lone pairs
The file contained 3 atoms not in residue templates
> check rna
Checking 'rna'....
Warning: There is a bond of 6.895 angstroms between O3' and P atoms:
------- .R<G 61>.A<O3' 34> and .R<G 62>.A<P 1>
Warning: The unperturbed charge of the unit (-66.000000) is not zero.
FATAL: Atom .R<C5 1>.A<P 30> does not have a type.
FATAL: Atom .R<C5 1>.A<OP1 31> does not have a type.
FATAL: Atom .R<C5 1>.A<OP2 32> does not have a type.
Warning: Close contact of 1.489340 angstroms between .R<C5 1>.A<H42 19> and
.R<C5 1>.A<H41 18>
Warning: Close contact of 0.640610 angstroms between .R<C5 1>.A<HO5' 1> and
.R<C5 1>.A<P 30>
Warning: Close contact of 1.485909 angstroms between .R<C5 1>.A<P 30> and
.R<C5 1>.A<OP1 31>
Warning: Close contact of 1.487235 angstroms between .R<C5 1>.A<P 30> and
.R<C5 1>.A<OP2 32>
Warning: Close contact of 1.489508 angstroms between .R<G 2>.A<H22 25> and
.R<G 2>.A<H21 24>
Warning: Close contact of 1.489822 angstroms between .R<G 3>.A<H22 25> and
.R<G 3>.A<H21 24>
Warning: Close contact of 1.490016 angstroms between .R<G 4>.A<H22 25> and
.R<G 4>.A<H21 24>
Warning: Close contact of 1.489291 angstroms between .R<C 5>.A<H42 21> and
.R<C 5>.A<H41 20>
Warning: Close contact of 1.489932 angstroms between .R<G 7>.A<H22 25> and
.R<G 7>.A<H21 24>
Warning: Close contact of 1.489264 angstroms between .R<A 8>.A<H62 21> and
.R<A 8>.A<H61 20>
Warning: Close contact of 1.489219 angstroms between .R<C 9>.A<H42 21> and
.R<C 9>.A<H41 20>
Warning: Close contact of 1.489504 angstroms between .R<C 10>.A<H42 21> and
.R<C 10>.A<H41 20>
Warning: Close contact of 1.489618 angstroms between .R<G 11>.A<H22 25> and
.R<G 11>.A<H21 24>
Warning: Close contact of 1.489743 angstroms between .R<A 12>.A<H62 21> and
.R<A 12>.A<H61 20>
Warning: Close contact of 1.489576 angstroms between .R<C 13>.A<H42 21> and
.R<C 13>.A<H41 20>
Warning: Close contact of 1.489203 angstroms between .R<C 14>.A<H42 21> and
.R<C 14>.A<H41 20>
Warning: Close contact of 1.489772 angstroms between .R<C 15>.A<H42 21> and
.R<C 15>.A<H41 20>
Warning: Close contact of 1.489907 angstroms between .R<C 16>.A<H42 21> and
.R<C 16>.A<H41 20>
Warning: Close contact of 1.488949 angstroms between .R<C 17>.A<H42 21> and
.R<C 17>.A<H41 20>
Warning: Close contact of 1.488778 angstroms between .R<C 18>.A<H42 21> and
.R<C 18>.A<H41 20>
Warning: Close contact of 1.489611 angstroms between .R<G 19>.A<H22 25> and
.R<G 19>.A<H21 24>
Warning: Close contact of 1.490184 angstroms between .R<A 20>.A<H62 21> and
.R<A 20>.A<H61 20>
Warning: Close contact of 1.489246 angstroms between .R<G 21>.A<H22 25> and
.R<G 21>.A<H21 24>
Warning: Close contact of 1.489275 angstroms between .R<C 24>.A<H42 21> and
.R<C 24>.A<H41 20>
Warning: Close contact of 1.489418 angstroms between .R<G 25>.A<H22 25> and
.R<G 25>.A<H21 24>
Warning: Close contact of 1.489250 angstroms between .R<C 26>.A<H42 21> and
.R<C 26>.A<H41 20>
Warning: Close contact of 1.489645 angstroms between .R<C 28>.A<H42 21> and
.R<C 28>.A<H41 20>
Warning: Close contact of 1.488615 angstroms between .R<G 29>.A<H22 25> and
.R<G 29>.A<H21 24>
Warning: Close contact of 1.489783 angstroms between .R<G 30>.A<H22 25> and
.R<G 30>.A<H21 24>
Warning: Close contact of 1.490368 angstroms between .R<G 31>.A<H22 25> and
.R<G 31>.A<H21 24>
Warning: Close contact of 1.489773 angstroms between .R<G 32>.A<H22 25> and
.R<G 32>.A<H21 24>
Warning: Close contact of 1.489927 angstroms between .R<A 33>.A<H62 21> and
.R<A 33>.A<H61 20>
Warning: Close contact of 1.488610 angstroms between .R<C 34>.A<H42 21> and
.R<C 34>.A<H41 20>
Warning: Close contact of 1.489277 angstroms between .R<A 35>.A<H62 21> and
.R<A 35>.A<H61 20>
Warning: Close contact of 1.489857 angstroms between .R<A 36>.A<H62 21> and
.R<A 36>.A<H61 20>
Warning: Close contact of 1.489498 angstroms between .R<C 37>.A<H42 21> and
.R<C 37>.A<H41 20>
Warning: Close contact of 1.489799 angstroms between .R<A 39>.A<H62 21> and
.R<A 39>.A<H61 20>
Warning: Close contact of 1.490039 angstroms between .R<G 40>.A<H22 25> and
.R<G 40>.A<H21 24>
Warning: Close contact of 1.489685 angstroms between .R<A 41>.A<H62 21> and
.R<A 41>.A<H61 20>
Warning: Close contact of 1.489299 angstroms between .R<C 42>.A<H42 21> and
.R<C 42>.A<H41 20>
Warning: Close contact of 1.489860 angstroms between .R<A 43>.A<H62 21> and
.R<A 43>.A<H61 20>
Warning: Close contact of 1.489880 angstroms between .R<A 45>.A<H62 21> and
.R<A 45>.A<H61 20>
Warning: Close contact of 1.489118 angstroms between .R<C 46>.A<H42 21> and
.R<C 46>.A<H41 20>
Warning: Close contact of 1.490014 angstroms between .R<A 47>.A<H62 21> and
.R<A 47>.A<H61 20>
Warning: Close contact of 1.489371 angstroms between .R<G 48>.A<H22 25> and
.R<G 48>.A<H21 24>
Warning: Close contact of 1.489673 angstroms between .R<A 50>.A<H62 21> and
.R<A 50>.A<H61 20>
Warning: Close contact of 1.489227 angstroms between .R<G 52>.A<H22 25> and
.R<G 52>.A<H21 24>
Warning: Close contact of 1.489664 angstroms between .R<A 53>.A<H62 21> and
.R<A 53>.A<H61 20>
Warning: Close contact of 0.697746 angstroms between .R<A 54>.A<N3 25> and
.R<A 55>.A<H62 21>
Warning: Close contact of 1.437354 angstroms between .R<A 54>.A<N3 25> and
.R<A 55>.A<H61 20>
Warning: Close contact of 0.950873 angstroms between .R<A 54>.A<N3 25> and
.R<A 55>.A<N6 19>
Warning: Close contact of 1.210963 angstroms between .R<A 54>.A<C2 23> and
.R<A 55>.A<H62 21>
Warning: Close contact of 1.489012 angstroms between .R<A 54>.A<H62 21> and
.R<A 54>.A<H61 20>
Warning: Close contact of 1.489968 angstroms between .R<A 56>.A<H62 21> and
.R<A 56>.A<H61 20>
Warning: Close contact of 1.490407 angstroms between .R<A 58>.A<H62 21> and
.R<A 58>.A<H61 20>
Warning: Close contact of 1.489522 angstroms between .R<C 59>.A<H42 21> and
.R<C 59>.A<H41 20>
Warning: Close contact of 1.489977 angstroms between .R<G 61>.A<H22 25> and
.R<G 61>.A<H21 24>
Warning: Close contact of 1.489008 angstroms between .R<G 62>.A<H22 25> and
.R<G 62>.A<H21 24>
Warning: Close contact of 1.489682 angstroms between .R<C 63>.A<H42 21> and
.R<C 63>.A<H41 20>
Warning: Close contact of 1.489300 angstroms between .R<C 64>.A<H42 21> and
.R<C 64>.A<H41 20>
Warning: Close contact of 1.488759 angstroms between .R<C 65>.A<H42 21> and
.R<C 65>.A<H41 20>
Warning: Close contact of 1.490501 angstroms between .R<G 66>.A<H22 25> and
.R<G 66>.A<H21 24>
Warning: Close contact of 1.489503 angstroms between .R<C3 67>.A<H42 21>
and .R<C3 67>.A<H41 20>
Checking parameters for unit 'rna'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 3 Warnings: 65
How do I resolve the FATAL error and Warning messages generated?
On Wed, Dec 7, 2022 at 3:54 PM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Dear AMBER Experts,
>
> I am trying to generate topology and parameter files for an RNA molecule
> following this:
>
> tleap
>
> source leaprc.DNA.OL15
>
> source leaprc.water.opc
>
> rna = loadpdb file.pdb
>
> check rna
>
> .........
>
> However, at this point it throws a number of earnings and errors as could
> be seen in the log file attached. Specifically, the messages show:
>
>
>
> Warning: Unknown residue: G number: 1 type: Nonterminal
> Warning: Unknown residue: G number: 2 type: Nonterminal
> Warning: Unknown residue: G number: 3 type: Nonterminal
> Warning: Unknown residue: C number: 4 type: Nonterminal
> Warning: Unknown residue: U number: 5 type: Nonterminal
> Warning: Unknown residue: G number: 6 type: Nonterminal
> Warning: Unknown residue: A number: 7 type: Nonterminal
> Warning: Unknown residue: C number: 8 type: Nonterminal
> Warning: Unknown residue: C number: 9 type: Nonterminal
> Warning: Unknown residue: G number: 10 type: Nonterminal
> Warning: Unknown residue: A number: 11 type: Nonterminal
> Warning: Unknown residue: C number: 12 type: Nonterminal
> Warning: Unknown residue: C number: 13 type: Nonterminal
> Warning: Unknown residue: C number: 14 type: Nonterminal
> Warning: Unknown residue: C number: 15 type: Nonterminal
> Warning: Unknown residue: C number: 16 type: Nonterminal
> Warning: Unknown residue: C number: 17 type: Nonterminal
> Warning: Unknown residue: G number: 18 type: Nonterminal
> Warning: Unknown residue: A number: 19 type: Nonterminal
> Warning: Unknown residue: G number: 20 type: Nonterminal
> Warning: Unknown residue: U number: 21 type: Nonterminal
> Warning: Unknown residue: U number: 22 type: Nonterminal
> Warning: Unknown residue: C number: 23 type: Nonterminal
> Warning: Unknown residue: G number: 24 type: Nonterminal
> Warning: Unknown residue: C number: 25 type: Nonterminal
> Warning: Unknown residue: U number: 26 type: Nonterminal
> Warning: Unknown residue: C number: 27 type: Nonterminal
> Warning: Unknown residue: G number: 28 type: Nonterminal
> Warning: Unknown residue: G number: 29 type: Nonterminal
> Warning: Unknown residue: G number: 30 type: Nonterminal
>
>
> Warning: Close contact of 1.485909 angstroms between .R<C 1>.A<P 1> and
> .R<C 1>.A<OP1 2>
> Warning: Close contact of 1.487235 angstroms between .R<C 1>.A<P 1> and
> .R<C 1>.A<OP2 3>
> Warning: Close contact of 1.420043 angstroms between .R<C 1>.A<O5' 4> and
> .R<C 1>.A<C5' 5>
> Warning: Close contact of 0.969779 angstroms between .R<C 1>.A<C5' 5> and
> .R<C 1>.A<H5' 21>
> Warning: Close contact of 0.969347 angstroms between .R<C 1>.A<C5' 5> and
> .R<C 1>.A<H5'' 22>
> Warning: Close contact of 1.454329 angstroms between .R<C 1>.A<C4' 6> and
> .R<C 1>.A<O4' 7>
> Warning: Close contact of 0.969781 angstroms between .R<C 1>.A<C4' 6> and
> .R<C 1>.A<H4' 23>
> Warning: Close contact of 1.415164 angstroms between .R<C 1>.A<O4' 7> and
> .R<C 1>.A<C1' 12>
> Warning: Close contact of 1.413674 angstroms between .R<C 1>.A<C3' 8> and
> .R<C 1>.A<O3' 9>
> Warning: Close contact of 0.970062 angstroms between .R<C 1>.A<C3' 8> and
> .R<C 1>.A<H3' 24>
> Warning: Close contact of 1.420019 angstroms between .R<C 1>.A<C2' 10> and
> .R<C 1>.A<O2' 11>
> Warning: Close contact of 0.969646 angstroms between .R<C 1>.A<C2' 10> and
> .R<C 1>.A<H2' 25>
> Warning: Close contact of 0.839894 angstroms between .R<C 1>.A<O2' 11> and
> .R<C 1>.A<HO2' 26>
> Warning: Close contact of 1.478335 angstroms between .R<C 1>.A<C1' 12> and
> .R<C 1>.A<N1 13>
>
> FATAL: Atom .R<C 2>.A<P 1> does not have a type.
> FATAL: Atom .R<C 2>.A<OP1 2> does not have a type.
> FATAL: Atom .R<C 2>.A<OP2 3> does not have a type.
> FATAL: Atom .R<C 2>.A<O5' 4> does not have a type.
> FATAL: Atom .R<C 2>.A<C5' 5> does not have a type.
> FATAL: Atom .R<C 2>.A<C4' 6> does not have a type.
> FATAL: Atom .R<C 2>.A<O4' 7> does not have a type.
> FATAL: Atom .R<C 2>.A<C3' 8> does not have a type.
> FATAL: Atom .R<C 2>.A<O3' 9> does not have a type.
> FATAL: Atom .R<C 2>.A<C2' 10> does not have a type
>
>
> What am I doing incorrectly? Please advise.
>
>
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Received on Wed Dec 07 2022 - 13:30:03 PST
