AMBER Archive (2004)

Subject: AMBER: nucgen generated RNA duplex: leap problems

From: Arvind (arvind_at_mbu.iisc.ernet.in)
Date: Tue Apr 20 2004 - 06:44:37 CDT

Hi all,
i generated an Arnott A-RNA duplex with the sequence (CGCAAAUUUGCG) using
the following nuc.in file:

  NUC 1
R
C5 G C A A A U U U G G G3

  NUC 2
R
C5 G C A A A U U U G G G3

END
$ARNA

Next i inserted a TER card in the pdb file generated and loaded it into
leap using loadpdb. But when i use 'check unit' command, i get a lot of
'close contact' warnings. This is my leap.log file:

Log file: ./leap.log
> #
> # ----- leaprc for loading the 2002 pol. force field, no lone
pairs
> # assumes that any unspecified nucleic acids are RNA
> #
> # load atom type hybridizations
> #
> addAtomTypes {
> { "H" "H" "sp3" }
> { "HO" "H" "sp3" }
> { "HS" "H" "sp3" }
> { "H1" "H" "sp3" }
> { "H2" "H" "sp3" }
> { "H3" "H" "sp3" }
> { "H4" "H" "sp3" }
> { "H5" "H" "sp3" }
> { "HW" "H" "sp3" }
> { "HC" "H" "sp3" }
> { "HA" "H" "sp3" }
> { "HP" "H" "sp3" }
> { "OH" "O" "sp3" }
> { "OS" "O" "sp3" }
> { "O" "O" "sp2" }
> { "O2" "O" "sp2" }
> { "OW" "O" "sp3" }
> { "CT" "C" "sp3" }
> { "CH" "C" "sp3" }
> { "C2" "C" "sp3" }
> { "C3" "C" "sp3" }
> { "C" "C" "sp2" }
> { "C*" "C" "sp2" }
> { "CA" "C" "sp2" }
> { "CB" "C" "sp2" }
> { "CC" "C" "sp2" }
> { "CN" "C" "sp2" }
> { "CM" "C" "sp2" }
> { "CK" "C" "sp2" }
> { "CQ" "C" "sp2" }
> { "CD" "C" "sp2" }
> { "CE" "C" "sp2" }
> { "CF" "C" "sp2" }
> { "CG" "C" "sp2" }
> { "CP" "C" "sp2" }
> { "CI" "C" "sp2" }
> { "CJ" "C" "sp2" }
> { "CW" "C" "sp2" }
> { "CV" "C" "sp2" }
> { "CR" "C" "sp2" }
> { "CA" "C" "sp2" }
> { "CY" "C" "sp2" }
> { "C0" "C" "sp2" }
> { "MG" "Mg" "sp3" }
> { "N" "N" "sp2" }
> { "NA" "N" "sp2" }
> { "N2" "N" "sp2" }
> { "N*" "N" "sp2" }
> { "NP" "N" "sp2" }
> { "NQ" "N" "sp2" }
> { "NB" "N" "sp2" }
> { "NC" "N" "sp2" }
> { "NT" "N" "sp3" }
> { "N3" "N" "sp3" }
> { "S" "S" "sp3" }
> { "SH" "S" "sp3" }
> { "P" "P" "sp3" }
> { "LP" "" "sp3" }
> { "F" "F" "sp3" }
> { "CL" "Cl" "sp3" }
> { "BR" "Br" "sp3" }
> { "I" "I" "sp3" }
> { "FE" "Fe" "sp3" }
> # glycam
> { "OG" "O" "sp3" }
> { "OL" "O" "sp3" }
> { "AC" "C" "sp3" }
> { "EC" "C" "sp3" }
> }
> #
> #
> # Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat
Loading parameters: /usr/local/amber7/dat/leap/parm/parm99.dat
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
> #
> # Load DNA/RNA libraries
> #
> loadOff all_nucleic02.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic02.lib
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: RA
Loading: RA3
Loading: RA5
Loading: RAN
Loading: RC
Loading: RC3
Loading: RC5
Loading: RCN
Loading: RG
Loading: RG3
Loading: RG5
Loading: RGN
Loading: RU
Loading: RU3
Loading: RU5
Loading: RUN
> #
> # Load main chain and terminating
> # amino acid libraries.
> #
> loadOff all_amino02.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino02.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
> loadOff all_aminoct02.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct02.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NME
> loadOff all_aminont02.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont02.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
> #
> # Load ion library
> #
> loadOff ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: Na+
Loading: Rb+
> loadOff solvents.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: SPC
Loading: TIP4PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: WATBOX216
> HOH = TP3
> WAT = TP3
> #
> # Define the PDB name map for the amino acids and RNA.
> #
> addPdbResMap {
> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
> { 0 "GUA" "RG5" } { 1 "GUA" "RG3" } { "GUA" "RG" }
> { 0 "ADE" "RA5" } { 1 "ADE" "RA3" } { "ADE" "RA" }
> { 0 "CYT" "RC5" } { 1 "CYT" "RC3" } { "CYT" "RC" }
> { 0 "URA" "RU5" } { 1 "URA" "RU3" } { "URA" "RU" }
> { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }
> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" }
> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" }
> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" }
> { 0 "C5" "RC5" }
> { 0 "G5" "RG5" }
> { 0 "A5" "RA5" }
> { 0 "U5" "RU5" }
> { 1 "C3" "RC3" }
> { 1 "G3" "RG3" }
> { 1 "A3" "RA3" }
> { 1 "U3" "RU3" }
>
> }
>
> addPdbAtomMap {
> { "O5*" "O5'" }
> { "C5*" "C5'" }
> { "C4*" "C4'" }
> { "O4*" "O4'" }
> { "C3*" "C3'" }
> { "O3*" "O3'" }
> { "O2*" "O2'" }
> { "C2*" "C2'" }
> { "C1*" "C1'" }
> # old ff atom names -> new
> { "O1'" "O4'" }
> { "OA" "O1P" }
> { "OB" "O2P" }
> { "H2'" "H2'1" }
> { "HO2'" "HO'2" }
> { "H5*1" "H5'1" }
> { "H5*2" "H5'2" }
> { "H4*" "H4'" }
> { "H3*" "H3'" }
> { "H1*" "H1'" }
> { "H2*1" "H2'1" }
> { "HO*2" "HO'2" }
> }
>
> #
> # assumed that most often users will want to use HID
> #
> NHIS = NHID
> HIS = HID
> CHIS = CHID
>
> # translate RNA residue names:
>
> GUA = RG
> CYT = RC
> ADE = RA
> URA = RU

> model = loadpdb nucgen_A3U3_ter.pdb
Loading PDB file: ./nucgen_A3U3_ter.pdb
Matching PDB residue names to LEaP variables.
Mapped residue C5, term: Terminal/beginning, seq. number: 0 to: RC5.
Mapped residue G, term: Nonterminal, seq. number: 1 to: RG.
Mapped residue C, term: Nonterminal, seq. number: 2 to: RC.
Mapped residue A, term: Nonterminal, seq. number: 3 to: RA.
Mapped residue A, term: Nonterminal, seq. number: 4 to: RA.
Mapped residue A, term: Nonterminal, seq. number: 5 to: RA.
Mapped residue U, term: Nonterminal, seq. number: 6 to: RU.
Mapped residue U, term: Nonterminal, seq. number: 7 to: RU.
Mapped residue U, term: Nonterminal, seq. number: 8 to: RU.
Mapped residue G, term: Nonterminal, seq. number: 9 to: RG.
Mapped residue G, term: Nonterminal, seq. number: 10 to: RG.
Mapped residue G3, term: Terminal/last, seq. number: 11 to: RG3.
Mapped residue C5, term: Terminal/beginning, seq. number: 12 to: RC5.
Mapped residue G, term: Nonterminal, seq. number: 13 to: RG.
Mapped residue C, term: Nonterminal, seq. number: 14 to: RC.
Mapped residue A, term: Nonterminal, seq. number: 15 to: RA.
Mapped residue A, term: Nonterminal, seq. number: 16 to: RA.
Mapped residue A, term: Nonterminal, seq. number: 17 to: RA.
Mapped residue U, term: Nonterminal, seq. number: 18 to: RU.
Mapped residue U, term: Nonterminal, seq. number: 19 to: RU.
Mapped residue U, term: Nonterminal, seq. number: 20 to: RU.
Mapped residue G, term: Nonterminal, seq. number: 21 to: RG.
Mapped residue G, term: Nonterminal, seq. number: 22 to: RG.
Mapped residue G3, term: Terminal/last, seq. number: 23 to: RG3.
Joining RC5 - RG
Joining RG - RC
Joining RC - RA
Joining RA - RA
Joining RA - RA
Joining RA - RU
Joining RU - RU
Joining RU - RU
Joining RU - RG
Joining RG - RG
Joining RG - RG3
Joining RC5 - RG
Joining RG - RC
Joining RC - RA
Joining RA - RA
Joining RA - RA
Joining RA - RU
Joining RU - RU
Joining RU - RU
Joining RU - RG
Joining RG - RG
Joining RG - RG3
  total atoms in file: 564
  Leap added 208 missing atoms according to residue templates:
       208 H / lone pairs
> check model
Checking 'model'....
WARNING: The unperturbed charge of the unit: -22.000000 is not zero.
Warning: Close contact of 1.998597 angstroms between .R<RG 2>.A<H22 25>
and .R<RG 23>.A<H22 25>
Warning: Close contact of 2.106936 angstroms between .R<RG 2>.A<H22 25>
and .R<RG 23>.A<H21 24>
Warning: Close contact of 2.153430 angstroms between .R<RG 2>.A<H22 25>
and .R<RG 23>.A<N2 23>
Warning: Close contact of 2.108330 angstroms between .R<RG 2>.A<H21 24>
and .R<RG 23>.A<H22 25>
Warning: Close contact of 0.908261 angstroms between .R<RG 2>.A<H21 24>
and .R<RG 23>.A<N2 23>
Warning: Close contact of 1.083242 angstroms between .R<RG 2>.A<H21 24>
and .R<RG 23>.A<C2 22>
Warning: Close contact of 2.153045 angstroms between .R<RG 2>.A<N2 23> and
.R<RG 23>.A<H22 25>
Warning: Close contact of 0.907910 angstroms between .R<RG 2>.A<N2 23> and
.R<RG 23>.A<H21 24>
Warning: Close contact of 0.739936 angstroms between .R<RG 2>.A<N2 23> and
.R<RG 23>.A<N2 23>
Warning: Close contact of 1.084625 angstroms between .R<RG 2>.A<C2 22> and
.R<RG 23>.A<H21 24>
Warning: Close contact of 0.769025 angstroms between .R<RG 2>.A<H1 21> and
.R<RG 23>.A<H1 21>
Warning: Close contact of 0.073769 angstroms between .R<RG 2>.A<H1 21> and
.R<RG 23>.A<N1 20>
Warning: Close contact of 1.904369 angstroms between .R<RG 2>.A<H1 21> and
.R<RG 23>.A<C6 18>
Warning: Close contact of 0.073645 angstroms between .R<RG 2>.A<N1 20> and
.R<RG 23>.A<H1 21>
Warning: Close contact of 1.322085 angstroms between .R<RG 2>.A<N1 20> and
.R<RG 23>.A<N1 20>
Warning: Close contact of 1.903981 angstroms between .R<RG 2>.A<C6 18> and
.R<RG 23>.A<H1 21>
Warning: Close contact of 1.998522 angstroms between .R<RG 11>.A<H22 25>
and .R<RG 14>.A<H22 25>
Warning: Close contact of 2.106002 angstroms between .R<RG 11>.A<H22 25>
and .R<RG 14>.A<H21 24>
Warning: Close contact of 2.152897 angstroms between .R<RG 11>.A<H22 25>
and .R<RG 14>.A<N2 23>
Warning: Close contact of 2.106756 angstroms between .R<RG 11>.A<H21 24>
and .R<RG 14>.A<H22 25>
Warning: Close contact of 0.908289 angstroms between .R<RG 11>.A<H21 24>
and .R<RG 14>.A<N2 23>
Warning: Close contact of 1.084493 angstroms between .R<RG 11>.A<H21 24>
and .R<RG 14>.A<C2 22>
Warning: Close contact of 2.152692 angstroms between .R<RG 11>.A<N2 23>
and .R<RG 14>.A<H22 25>
Warning: Close contact of 0.907480 angstroms between .R<RG 11>.A<N2 23>
and .R<RG 14>.A<H21 24>
Warning: Close contact of 0.740137 angstroms between .R<RG 11>.A<N2 23>
and .R<RG 14>.A<N2 23>
Warning: Close contact of 1.083588 angstroms between .R<RG 11>.A<C2 22>
and .R<RG 14>.A<H21 24>
Warning: Close contact of 0.769885 angstroms between .R<RG 11>.A<H1 21>
and .R<RG 14>.A<H1 21>
Warning: Close contact of 0.073941 angstroms between .R<RG 11>.A<H1 21>
and .R<RG 14>.A<N1 20>
Warning: Close contact of 1.903058 angstroms between .R<RG 11>.A<H1 21>
and .R<RG 14>.A<C6 18>
Warning: Close contact of 0.073769 angstroms between .R<RG 11>.A<N1 20>
and .R<RG 14>.A<H1 21>
Warning: Close contact of 1.322481 angstroms between .R<RG 11>.A<N1 20>
and .R<RG 14>.A<N1 20>
Warning: Close contact of 1.902241 angstroms between .R<RG 11>.A<C6 18>
and .R<RG 14>.A<H1 21>
Checking parameters for unit 'model'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 33
Unit is OK.
> quit
        Quit

It seems a lot of atoms are coming closer than they ought to be,
physically. Why is these happening? I guess these would create problems
later. Can somebody suggest me a way to get rid of these errors?
Thanx in advance.

Regards,
Arvind.

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