AMBER Archive (2009)

Subject: [AMBER] "loadoff tRNA.lib" in Leap

From: Ju Zhang (xju.zhang_at_gmail.com)
Date: Tue Jun 23 2009 - 15:55:25 CDT

Dear all,

I am trying to load the pdb file of tRNA-phe (4TRA.pdb) into xleap,
and I found tRNA.lib with the parameters for non-standard residues is
already available with Amber10.

However, when I tried load the library file (loadoff tRNA.lib), xleap
gave me the message --
"
...
...
Loading: 5GP

Bond: Maximum coordination exceeded on A<H5T 36>

     -- setting atoms pert=true overrides default limits

...
...
"
Then after I load the pdb file (mol1 = loadpdb "4TRA.pdb"), I got the
messages indicating that Leap failed to recognize the modified
residues.

I also checked the archive letters, and from one of Dave Case's
responses, I noticed that the library file was generated by adding a
artifitial P-H bond in 5GP to fix the geometry of the terminal P-O-P
group. My question is what does this message mean, what is pert=true
and how can I set that?

Is that the reason that when I load the tRNA pdb file, the 4TRA.pdb is
not recognized? All the related leap.log info is attached below.

Thank you very much!

Ju Zhang

-----------------------------------
> loadoff tRNA.lib

Loading library: ./tRNA.lib

Loading: 1MA

Loading: 2MG

Loading: 5GP

Bond: Maximum coordination exceeded on A<H5T 36>

     -- setting atoms pert=true overrides default limits

Loading: 5MC

Loading: 5MU

Loading: 7MG

Loading: H2U

Loading: M2G

Loading: Mg+

Loading: OMC

Loading: OMG

Loading: PSU

Loading: SPM

Loading: YG

> mol1 = loadpdb "4TRA.pdb"

Loading PDB file: ./4TRA.pdb

Enter zPdbReadScan from call depth 0.

Exit zPdbReadScan from call depth 0.

Matching PDB residue names to LEaP variables.

Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5.

Mapped residue C, term: Nonterminal, seq. number: 1 to: RC.

Mapped residue G, term: Nonterminal, seq. number: 2 to: RG.

Mapped residue G, term: Nonterminal, seq. number: 3 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 4 to: RA.

Mapped residue U, term: Nonterminal, seq. number: 5 to: RU.

Mapped residue U, term: Nonterminal, seq. number: 6 to: RU.

Mapped residue U, term: Nonterminal, seq. number: 7 to: RU.

Mapped residue A, term: Nonterminal, seq. number: 8 to: RA.

(Residue 9: 2MG, Nonterminal, was not found in name map.)

Mapped residue C, term: Nonterminal, seq. number: 10 to: RC.

Mapped residue U, term: Nonterminal, seq. number: 11 to: RU.

Mapped residue C, term: Nonterminal, seq. number: 12 to: RC.

Mapped residue A, term: Nonterminal, seq. number: 13 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 14 to: RG.

(Residue 15: H2U, Nonterminal, was not found in name map.)

(Residue 16: H2U, Nonterminal, was not found in name map.)

Mapped residue G, term: Nonterminal, seq. number: 17 to: RG.

Mapped residue G, term: Nonterminal, seq. number: 18 to: RG.

Mapped residue G, term: Nonterminal, seq. number: 19 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 20 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 21 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 22 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 23 to: RG.

Mapped residue C, term: Nonterminal, seq. number: 24 to: RC.

(Residue 25: M2G, Nonterminal, was not found in name map.)

Mapped residue C, term: Nonterminal, seq. number: 26 to: RC.

Mapped residue C, term: Nonterminal, seq. number: 27 to: RC.

Mapped residue A, term: Nonterminal, seq. number: 28 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 29 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 30 to: RA.

(Residue 31: OMC, Nonterminal, was not found in name map.)

Mapped residue U, term: Nonterminal, seq. number: 32 to: RU.

(Residue 33: OMG, Nonterminal, was not found in name map.)

Mapped residue A, term: Nonterminal, seq. number: 34 to: RA.

Mapped residue A, term: Nonterminal, seq. number: 35 to: RA.

(Residue 36: YG, Nonterminal, was not found in name map.)

Mapped residue A, term: Nonterminal, seq. number: 37 to: RA.

(Residue 38: PSU, Nonterminal, was not found in name map.)

(Residue 39: 5MC, Nonterminal, was not found in name map.)

Mapped residue U, term: Nonterminal, seq. number: 40 to: RU.

Mapped residue G, term: Nonterminal, seq. number: 41 to: RG.

Mapped residue G, term: Nonterminal, seq. number: 42 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 43 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 44 to: RG.

(Residue 45: 7MG, Nonterminal, was not found in name map.)

Mapped residue U, term: Nonterminal, seq. number: 46 to: RU.

Mapped residue C, term: Nonterminal, seq. number: 47 to: RC.

(Residue 48: 5MC, Nonterminal, was not found in name map.)

Mapped residue U, term: Nonterminal, seq. number: 49 to: RU.

Mapped residue G, term: Nonterminal, seq. number: 50 to: RG.

Mapped residue U, term: Nonterminal, seq. number: 51 to: RU.

Mapped residue G, term: Nonterminal, seq. number: 52 to: RG.

(Residue 53: 5MU, Nonterminal, was not found in name map.)

(Residue 54: PSU, Nonterminal, was not found in name map.)

Mapped residue C, term: Nonterminal, seq. number: 55 to: RC.

Mapped residue G, term: Nonterminal, seq. number: 56 to: RG.

(Residue 57: 1MA, Nonterminal, was not found in name map.)

Mapped residue U, term: Nonterminal, seq. number: 58 to: RU.

Mapped residue C, term: Nonterminal, seq. number: 59 to: RC.

Mapped residue C, term: Nonterminal, seq. number: 60 to: RC.

Mapped residue A, term: Nonterminal, seq. number: 61 to: RA.

Mapped residue C, term: Nonterminal, seq. number: 62 to: RC.

Mapped residue A, term: Nonterminal, seq. number: 63 to: RA.

Mapped residue G, term: Nonterminal, seq. number: 64 to: RG.

Mapped residue A, term: Nonterminal, seq. number: 65 to: RA.

Mapped residue A, term: Nonterminal, seq. number: 66 to: RA.

Mapped residue U, term: Nonterminal, seq. number: 67 to: RU.

Mapped residue U, term: Nonterminal, seq. number: 68 to: RU.

Mapped residue C, term: Nonterminal, seq. number: 69 to: RC.

Mapped residue G, term: Nonterminal, seq. number: 70 to: RG.

Mapped residue C, term: Nonterminal, seq. number: 71 to: RC.

Mapped residue A, term: Nonterminal, seq. number: 72 to: RA.

Mapped residue C, term: Nonterminal, seq. number: 73 to: RC.

Mapped residue C, term: Nonterminal, seq. number: 74 to: RC.

Mapped residue A, term: Terminal/last, seq. number: 75 to: RA3.

Created a new atom named: OP3 within residue: .R<RG5 1>

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

Created a new atom named: OP1 within residue: .R<RG5 1>

Created a new atom named: OP2 within residue: .R<RG5 1>

Joining RG5 - RC

Created a new atom named: OP1 within residue: .R<RC 2>

Created a new atom named: OP2 within residue: .R<RC 2>

 Added missing heavy atom: .R<RC 2>.A<O1P 2>

 Added missing heavy atom: .R<RC 2>.A<O2P 3>

Joining RC - RG

Created a new atom named: OP1 within residue: .R<RG 3>

Created a new atom named: OP2 within residue: .R<RG 3>

 Added missing heavy atom: .R<RG 3>.A<O1P 2>

 Added missing heavy atom: .R<RG 3>.A<O2P 3>

Joining RG - RG

Created a new atom named: OP1 within residue: .R<RG 4>

Created a new atom named: OP2 within residue: .R<RG 4>

 Added missing heavy atom: .R<RG 4>.A<O1P 2>

 Added missing heavy atom: .R<RG 4>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 5>

Created a new atom named: OP2 within residue: .R<RA 5>

 Added missing heavy atom: .R<RA 5>.A<O1P 2>

 Added missing heavy atom: .R<RA 5>.A<O2P 3>

Joining RA - RU

Created a new atom named: OP1 within residue: .R<RU 6>

Created a new atom named: OP2 within residue: .R<RU 6>

 Added missing heavy atom: .R<RU 6>.A<O1P 2>

 Added missing heavy atom: .R<RU 6>.A<O2P 3>

Joining RU - RU

Created a new atom named: OP1 within residue: .R<RU 7>

Created a new atom named: OP2 within residue: .R<RU 7>

 Added missing heavy atom: .R<RU 7>.A<O1P 2>

 Added missing heavy atom: .R<RU 7>.A<O2P 3>

Joining RU - RU

Created a new atom named: OP1 within residue: .R<RU 8>

Created a new atom named: OP2 within residue: .R<RU 8>

 Added missing heavy atom: .R<RU 8>.A<O1P 2>

 Added missing heavy atom: .R<RU 8>.A<O2P 3>

Joining RU - RA

Created a new atom named: OP1 within residue: .R<RA 9>

Created a new atom named: OP2 within residue: .R<RA 9>

 Added missing heavy atom: .R<RA 9>.A<O1P 2>

 Added missing heavy atom: .R<RA 9>.A<O2P 3>

Joining RA - 2MG

Created a new atom named: OP1 within residue: .R<2MG 10>

Created a new atom named: OP2 within residue: .R<2MG 10>

 Added missing heavy atom: .R<2MG 10>.A<O1P 24>

 Added missing heavy atom: .R<2MG 10>.A<O2P 25>

Joining 2MG - RC

Created a new atom named: OP1 within residue: .R<RC 11>

Created a new atom named: OP2 within residue: .R<RC 11>

 Added missing heavy atom: .R<RC 11>.A<O1P 2>

 Added missing heavy atom: .R<RC 11>.A<O2P 3>

Joining RC - RU

Created a new atom named: OP1 within residue: .R<RU 12>

Created a new atom named: OP2 within residue: .R<RU 12>

 Added missing heavy atom: .R<RU 12>.A<O1P 2>

 Added missing heavy atom: .R<RU 12>.A<O2P 3>

Joining RU - RC

Created a new atom named: OP1 within residue: .R<RC 13>

Created a new atom named: OP2 within residue: .R<RC 13>

 Added missing heavy atom: .R<RC 13>.A<O1P 2>

 Added missing heavy atom: .R<RC 13>.A<O2P 3>

Joining RC - RA

Created a new atom named: OP1 within residue: .R<RA 14>

Created a new atom named: OP2 within residue: .R<RA 14>

 Added missing heavy atom: .R<RA 14>.A<O1P 2>

 Added missing heavy atom: .R<RA 14>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 15>

Created a new atom named: OP2 within residue: .R<RG 15>

 Added missing heavy atom: .R<RG 15>.A<O1P 2>

 Added missing heavy atom: .R<RG 15>.A<O2P 3>

Joining RG - H2U

Created a new atom named: OP1 within residue: .R<H2U 16>

Created a new atom named: OP2 within residue: .R<H2U 16>

 Added missing heavy atom: .R<H2U 16>.A<O1P 19>

 Added missing heavy atom: .R<H2U 16>.A<O2P 20>

Joining H2U - H2U

Created a new atom named: OP1 within residue: .R<H2U 17>

Created a new atom named: OP2 within residue: .R<H2U 17>

 Added missing heavy atom: .R<H2U 17>.A<O1P 19>

 Added missing heavy atom: .R<H2U 17>.A<O2P 20>

Joining H2U - RG

Created a new atom named: OP1 within residue: .R<RG 18>

Created a new atom named: OP2 within residue: .R<RG 18>

 Added missing heavy atom: .R<RG 18>.A<O1P 2>

 Added missing heavy atom: .R<RG 18>.A<O2P 3>

Joining RG - RG

Created a new atom named: OP1 within residue: .R<RG 19>

Created a new atom named: OP2 within residue: .R<RG 19>

 Added missing heavy atom: .R<RG 19>.A<O1P 2>

 Added missing heavy atom: .R<RG 19>.A<O2P 3>

Joining RG - RG

Created a new atom named: OP1 within residue: .R<RG 20>

Created a new atom named: OP2 within residue: .R<RG 20>

 Added missing heavy atom: .R<RG 20>.A<O1P 2>

 Added missing heavy atom: .R<RG 20>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 21>

Created a new atom named: OP2 within residue: .R<RA 21>

 Added missing heavy atom: .R<RA 21>.A<O1P 2>

 Added missing heavy atom: .R<RA 21>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 22>

Created a new atom named: OP2 within residue: .R<RG 22>

 Added missing heavy atom: .R<RG 22>.A<O1P 2>

 Added missing heavy atom: .R<RG 22>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 23>

Created a new atom named: OP2 within residue: .R<RA 23>

 Added missing heavy atom: .R<RA 23>.A<O1P 2>

 Added missing heavy atom: .R<RA 23>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 24>

Created a new atom named: OP2 within residue: .R<RG 24>

 Added missing heavy atom: .R<RG 24>.A<O1P 2>

 Added missing heavy atom: .R<RG 24>.A<O2P 3>

Joining RG - RC

Created a new atom named: OP1 within residue: .R<RC 25>

Created a new atom named: OP2 within residue: .R<RC 25>

 Added missing heavy atom: .R<RC 25>.A<O1P 2>

 Added missing heavy atom: .R<RC 25>.A<O2P 3>

Joining RC - M2G

Created a new atom named: OP1 within residue: .R<M2G 26>

Created a new atom named: OP2 within residue: .R<M2G 26>

 Added missing heavy atom: .R<M2G 26>.A<O1P 27>

 Added missing heavy atom: .R<M2G 26>.A<O2P 28>

Joining M2G - RC

Created a new atom named: OP1 within residue: .R<RC 27>

Created a new atom named: OP2 within residue: .R<RC 27>

 Added missing heavy atom: .R<RC 27>.A<O1P 2>

 Added missing heavy atom: .R<RC 27>.A<O2P 3>

Joining RC - RC

Created a new atom named: OP1 within residue: .R<RC 28>

Created a new atom named: OP2 within residue: .R<RC 28>

 Added missing heavy atom: .R<RC 28>.A<O1P 2>

 Added missing heavy atom: .R<RC 28>.A<O2P 3>

Joining RC - RA

Created a new atom named: OP1 within residue: .R<RA 29>

Created a new atom named: OP2 within residue: .R<RA 29>

 Added missing heavy atom: .R<RA 29>.A<O1P 2>

 Added missing heavy atom: .R<RA 29>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 30>

Created a new atom named: OP2 within residue: .R<RG 30>

 Added missing heavy atom: .R<RG 30>.A<O1P 2>

 Added missing heavy atom: .R<RG 30>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 31>

Created a new atom named: OP2 within residue: .R<RA 31>

 Added missing heavy atom: .R<RA 31>.A<O1P 2>

 Added missing heavy atom: .R<RA 31>.A<O2P 3>

Joining RA - OMC

Created a new atom named: OP1 within residue: .R<OMC 32>

Created a new atom named: OP2 within residue: .R<OMC 32>

 Added missing heavy atom: .R<OMC 32>.A<O1P 2>

 Added missing heavy atom: .R<OMC 32>.A<O2P 3>

Joining OMC - RU

Created a new atom named: OP1 within residue: .R<RU 33>

Created a new atom named: OP2 within residue: .R<RU 33>

 Added missing heavy atom: .R<RU 33>.A<O1P 2>

 Added missing heavy atom: .R<RU 33>.A<O2P 3>

Joining RU - OMG

Created a new atom named: OP1 within residue: .R<OMG 34>

Created a new atom named: OP2 within residue: .R<OMG 34>

 Added missing heavy atom: .R<OMG 34>.A<O1P 2>

 Added missing heavy atom: .R<OMG 34>.A<O2P 3>

Joining OMG - RA

Created a new atom named: OP1 within residue: .R<RA 35>

Created a new atom named: OP2 within residue: .R<RA 35>

 Added missing heavy atom: .R<RA 35>.A<O1P 2>

 Added missing heavy atom: .R<RA 35>.A<O2P 3>

Joining RA - RA

Created a new atom named: OP1 within residue: .R<RA 36>

Created a new atom named: OP2 within residue: .R<RA 36>

 Added missing heavy atom: .R<RA 36>.A<O1P 2>

 Added missing heavy atom: .R<RA 36>.A<O2P 3>

Joining RA - YG

Created a new atom named: OP1 within residue: .R<YG 37>

Created a new atom named: OP2 within residue: .R<YG 37>

 Added missing heavy atom: .R<YG 37>.A<O1P 49>

 Added missing heavy atom: .R<YG 37>.A<O2P 50>

Joining YG - RA

Created a new atom named: OP1 within residue: .R<RA 38>

Created a new atom named: OP2 within residue: .R<RA 38>

 Added missing heavy atom: .R<RA 38>.A<O1P 2>

 Added missing heavy atom: .R<RA 38>.A<O2P 3>

Joining RA - PSU

Created a new atom named: OP1 within residue: .R<PSU 39>

Created a new atom named: OP2 within residue: .R<PSU 39>

 Added missing heavy atom: .R<PSU 39>.A<O1P 13>

 Added missing heavy atom: .R<PSU 39>.A<O2P 14>

Joining PSU - 5MC

Created a new atom named: OP1 within residue: .R<5MC 40>

Created a new atom named: OP2 within residue: .R<5MC 40>

 Added missing heavy atom: .R<5MC 40>.A<O1P 21>

 Added missing heavy atom: .R<5MC 40>.A<O2P 22>

Joining 5MC - RU

Created a new atom named: OP1 within residue: .R<RU 41>

Created a new atom named: OP2 within residue: .R<RU 41>

 Added missing heavy atom: .R<RU 41>.A<O1P 2>

 Added missing heavy atom: .R<RU 41>.A<O2P 3>

Joining RU - RG

Created a new atom named: OP1 within residue: .R<RG 42>

Created a new atom named: OP2 within residue: .R<RG 42>

 Added missing heavy atom: .R<RG 42>.A<O1P 2>

 Added missing heavy atom: .R<RG 42>.A<O2P 3>

Joining RG - RG

Created a new atom named: OP1 within residue: .R<RG 43>

Created a new atom named: OP2 within residue: .R<RG 43>

 Added missing heavy atom: .R<RG 43>.A<O1P 2>

 Added missing heavy atom: .R<RG 43>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 44>

Created a new atom named: OP2 within residue: .R<RA 44>

 Added missing heavy atom: .R<RA 44>.A<O1P 2>

 Added missing heavy atom: .R<RA 44>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 45>

Created a new atom named: OP2 within residue: .R<RG 45>

 Added missing heavy atom: .R<RG 45>.A<O1P 2>

 Added missing heavy atom: .R<RG 45>.A<O2P 3>

Joining RG - 7MG

Created a new atom named: OP1 within residue: .R<7MG 46>

Created a new atom named: OP2 within residue: .R<7MG 46>

 Added missing heavy atom: .R<7MG 46>.A<O1P 26>

 Added missing heavy atom: .R<7MG 46>.A<O2P 27>

Joining 7MG - RU

Created a new atom named: OP1 within residue: .R<RU 47>

Created a new atom named: OP2 within residue: .R<RU 47>

 Added missing heavy atom: .R<RU 47>.A<O1P 2>

 Added missing heavy atom: .R<RU 47>.A<O2P 3>

Joining RU - RC

Created a new atom named: OP1 within residue: .R<RC 48>

Created a new atom named: OP2 within residue: .R<RC 48>

 Added missing heavy atom: .R<RC 48>.A<O1P 2>

 Added missing heavy atom: .R<RC 48>.A<O2P 3>

Joining RC - 5MC

Created a new atom named: OP1 within residue: .R<5MC 49>

Created a new atom named: OP2 within residue: .R<5MC 49>

 Added missing heavy atom: .R<5MC 49>.A<O1P 21>

 Added missing heavy atom: .R<5MC 49>.A<O2P 22>

Joining 5MC - RU

Created a new atom named: OP1 within residue: .R<RU 50>

Created a new atom named: OP2 within residue: .R<RU 50>

 Added missing heavy atom: .R<RU 50>.A<O1P 2>

 Added missing heavy atom: .R<RU 50>.A<O2P 3>

Joining RU - RG

Created a new atom named: OP1 within residue: .R<RG 51>

Created a new atom named: OP2 within residue: .R<RG 51>

 Added missing heavy atom: .R<RG 51>.A<O1P 2>

 Added missing heavy atom: .R<RG 51>.A<O2P 3>

Joining RG - RU

Created a new atom named: OP1 within residue: .R<RU 52>

Created a new atom named: OP2 within residue: .R<RU 52>

 Added missing heavy atom: .R<RU 52>.A<O1P 2>

 Added missing heavy atom: .R<RU 52>.A<O2P 3>

Joining RU - RG

Created a new atom named: OP1 within residue: .R<RG 53>

Created a new atom named: OP2 within residue: .R<RG 53>

 Added missing heavy atom: .R<RG 53>.A<O1P 2>

 Added missing heavy atom: .R<RG 53>.A<O2P 3>

Joining RG - 5MU

Created a new atom named: OP1 within residue: .R<5MU 54>

Created a new atom named: OP2 within residue: .R<5MU 54>

 Added missing heavy atom: .R<5MU 54>.A<O1P 20>

 Added missing heavy atom: .R<5MU 54>.A<O2P 21>

Joining 5MU - PSU

Created a new atom named: OP1 within residue: .R<PSU 55>

Created a new atom named: OP2 within residue: .R<PSU 55>

 Added missing heavy atom: .R<PSU 55>.A<O1P 13>

 Added missing heavy atom: .R<PSU 55>.A<O2P 14>

Joining PSU - RC

Created a new atom named: OP1 within residue: .R<RC 56>

Created a new atom named: OP2 within residue: .R<RC 56>

 Added missing heavy atom: .R<RC 56>.A<O1P 2>

 Added missing heavy atom: .R<RC 56>.A<O2P 3>

Joining RC - RG

Created a new atom named: OP1 within residue: .R<RG 57>

Created a new atom named: OP2 within residue: .R<RG 57>

 Added missing heavy atom: .R<RG 57>.A<O1P 2>

 Added missing heavy atom: .R<RG 57>.A<O2P 3>

Joining RG - 1MA

Created a new atom named: OP1 within residue: .R<1MA 58>

Created a new atom named: OP2 within residue: .R<1MA 58>

 Added missing heavy atom: .R<1MA 58>.A<O1P 25>

 Added missing heavy atom: .R<1MA 58>.A<O2P 26>

Joining 1MA - RU

Created a new atom named: OP1 within residue: .R<RU 59>

Created a new atom named: OP2 within residue: .R<RU 59>

 Added missing heavy atom: .R<RU 59>.A<O1P 2>

 Added missing heavy atom: .R<RU 59>.A<O2P 3>

Joining RU - RC

Created a new atom named: OP1 within residue: .R<RC 60>

Created a new atom named: OP2 within residue: .R<RC 60>

 Added missing heavy atom: .R<RC 60>.A<O1P 2>

 Added missing heavy atom: .R<RC 60>.A<O2P 3>

Joining RC - RC

Created a new atom named: OP1 within residue: .R<RC 61>

Created a new atom named: OP2 within residue: .R<RC 61>

 Added missing heavy atom: .R<RC 61>.A<O1P 2>

 Added missing heavy atom: .R<RC 61>.A<O2P 3>

Joining RC - RA

Created a new atom named: OP1 within residue: .R<RA 62>

Created a new atom named: OP2 within residue: .R<RA 62>

 Added missing heavy atom: .R<RA 62>.A<O1P 2>

 Added missing heavy atom: .R<RA 62>.A<O2P 3>

Joining RA - RC

Created a new atom named: OP1 within residue: .R<RC 63>

Created a new atom named: OP2 within residue: .R<RC 63>

 Added missing heavy atom: .R<RC 63>.A<O1P 2>

 Added missing heavy atom: .R<RC 63>.A<O2P 3>

Joining RC - RA

Created a new atom named: OP1 within residue: .R<RA 64>

Created a new atom named: OP2 within residue: .R<RA 64>

 Added missing heavy atom: .R<RA 64>.A<O1P 2>

 Added missing heavy atom: .R<RA 64>.A<O2P 3>

Joining RA - RG

Created a new atom named: OP1 within residue: .R<RG 65>

Created a new atom named: OP2 within residue: .R<RG 65>

 Added missing heavy atom: .R<RG 65>.A<O1P 2>

 Added missing heavy atom: .R<RG 65>.A<O2P 3>

Joining RG - RA

Created a new atom named: OP1 within residue: .R<RA 66>

Created a new atom named: OP2 within residue: .R<RA 66>

 Added missing heavy atom: .R<RA 66>.A<O1P 2>

 Added missing heavy atom: .R<RA 66>.A<O2P 3>

Joining RA - RA

Created a new atom named: OP1 within residue: .R<RA 67>

Created a new atom named: OP2 within residue: .R<RA 67>

 Added missing heavy atom: .R<RA 67>.A<O1P 2>

 Added missing heavy atom: .R<RA 67>.A<O2P 3>

Joining RA - RU

Created a new atom named: OP1 within residue: .R<RU 68>

Created a new atom named: OP2 within residue: .R<RU 68>

 Added missing heavy atom: .R<RU 68>.A<O1P 2>

 Added missing heavy atom: .R<RU 68>.A<O2P 3>

Joining RU - RU

Created a new atom named: OP1 within residue: .R<RU 69>

Created a new atom named: OP2 within residue: .R<RU 69>

 Added missing heavy atom: .R<RU 69>.A<O1P 2>

 Added missing heavy atom: .R<RU 69>.A<O2P 3>

Joining RU - RC

Created a new atom named: OP1 within residue: .R<RC 70>

Created a new atom named: OP2 within residue: .R<RC 70>

 Added missing heavy atom: .R<RC 70>.A<O1P 2>

 Added missing heavy atom: .R<RC 70>.A<O2P 3>

Joining RC - RG

Created a new atom named: OP1 within residue: .R<RG 71>

Created a new atom named: OP2 within residue: .R<RG 71>

 Added missing heavy atom: .R<RG 71>.A<O1P 2>

 Added missing heavy atom: .R<RG 71>.A<O2P 3>

Joining RG - RC

Created a new atom named: OP1 within residue: .R<RC 72>

Created a new atom named: OP2 within residue: .R<RC 72>

 Added missing heavy atom: .R<RC 72>.A<O1P 2>

 Added missing heavy atom: .R<RC 72>.A<O2P 3>

Joining RC - RA

Created a new atom named: OP1 within residue: .R<RA 73>

Created a new atom named: OP2 within residue: .R<RA 73>

 Added missing heavy atom: .R<RA 73>.A<O1P 2>

 Added missing heavy atom: .R<RA 73>.A<O2P 3>

Joining RA - RC

Created a new atom named: OP1 within residue: .R<RC 74>

Created a new atom named: OP2 within residue: .R<RC 74>

 Added missing heavy atom: .R<RC 74>.A<O1P 2>

 Added missing heavy atom: .R<RC 74>.A<O2P 3>

Joining RC - RC

Created a new atom named: OP1 within residue: .R<RC 75>

Created a new atom named: OP2 within residue: .R<RC 75>

 Added missing heavy atom: .R<RC 75>.A<O1P 2>

 Added missing heavy atom: .R<RC 75>.A<O2P 3>

Joining RC - RA3

Created a new atom named: OP1 within residue: .R<RA3 76>

Created a new atom named: OP2 within residue: .R<RA3 76>

 Added missing heavy atom: .R<RA3 76>.A<O1P 2>

 Added missing heavy atom: .R<RA3 76>.A<O2P 3>

 total atoms in file: 1652

 Leap added 1011 missing atoms according to residue templates:

      150 Heavy

      861 H / lone pairs

 The file contained 154 atoms not in residue templates

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber