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
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Received on Mon Jul 06 2009 - 11:03:46 PDT
