AMBER Archive (2004)

Subject: Re: AMBER: Bad atom symbol, K+ and IB in vacuum

From: Skauge Tormod (Tormod.Skauge_at_kj.uib.no)
Date: Wed Mar 31 2004 - 06:20:30 CST

Hi Rhonda,

Thanks for a quick reply. True, the parm99.dat is taken from amber7 and
used with amber6. So I do get a prmtop and it looks ok both in xleap and
in VMD. The error message lead me to believe it was a problem with the
format and I shifted the IB input one column left. Then it reads "bad
atom symbol B". Apparently, it only reads the first letter and does not
recognize IB. Shifting "IB" to the right gives "bad atom symbol " (i.e.
blank). Adding Na+ works perfectly well. I've included the leap.log
below.

Thanks,
Tormod

leap.log:
----------------------------------------------------
log started: Mon Mar 29 16:47:57 2004

Log file: ./leap.log
> #
> # ----- leaprc for loading the Cornell et al. 1994 topologies
> # with parm99
> # 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/amber6/dat/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_nucleic94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_nucleic94.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_amino94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_amino94.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_aminoct94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminoct94.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_aminont94.lib
Loading library: /usr/local/amber6/dat/leap/lib/all_aminont94.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/amber6/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: Na+
Loading: Rb+
> loadOff solvents.lib
Could not open file solvents.lib: not found
Could not open database: solvents.lib
> 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
 
> toto = loadPDB "/home/tormod/rna/structure/GApU_duplex_vac_minH.pdb"
Loading PDB file: /home/tormod/rna/structure/GApU_duplex_vac_minH.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: RG5, Terminal/beginning, was not found in name map.)
(Residue 1: RC, Nonterminal, was not found in name map.)
(Residue 2: RG, Nonterminal, was not found in name map.)
(Residue 3: RU, Nonterminal, was not found in name map.)
(Residue 4: RU, Nonterminal, was not found in name map.)
(Residue 5: RU, Nonterminal, was not found in name map.)
(Residue 6: RG, Nonterminal, was not found in name map.)
(Residue 7: RA, Nonterminal, was not found in name map.)
(Residue 8: RA, Nonterminal, was not found in name map.)
(Residue 9: RA, Nonterminal, was not found in name map.)
(Residue 10: RC, Nonterminal, was not found in name map.)
(Residue 11: RG, Nonterminal, was not found in name map.)
(Residue 12: RC3, Terminal/last, was not found in name map.)
(Residue 13: RG5, Terminal/beginning, was not found in name map.)
(Residue 14: RC, Nonterminal, was not found in name map.)
(Residue 15: RG, Nonterminal, was not found in name map.)
(Residue 16: RU, Nonterminal, was not found in name map.)
(Residue 17: RU, Nonterminal, was not found in name map.)
(Residue 18: RU, Nonterminal, was not found in name map.)
(Residue 19: RG, Nonterminal, was not found in name map.)
(Residue 20: RA, Nonterminal, was not found in name map.)
(Residue 21: RA, Nonterminal, was not found in name map.)
(Residue 22: RA, Nonterminal, was not found in name map.)
(Residue 23: RC, Nonterminal, was not found in name map.)
(Residue 24: RG, Nonterminal, was not found in name map.)
(Residue 25: RC3, Terminal/last, was not found in name map.)
Joining RG5 - RC
Joining RC - RG
Joining RG - RU
Joining RU - RU
Joining RU - RU
Joining RU - RG
Joining RG - RA
Joining RA - RA
Joining RA - RA
Joining RA - RC
Joining RC - RG
Joining RG - RC3
Joining RG5 - RC
Joining RC - RG
Joining RG - RU
Joining RU - RU
Joining RU - RU
Joining RU - RG
Joining RG - RA
Joining RA - RA
Joining RA - RA
Joining RA - RC
Joining RC - RG
Joining RG - RC3
  total atoms in file: 834
> edit toto
Unit Editor: > check toto
Unit Editor: Checking 'toto'....
Unit Editor: WARNING: The unperturbed charge of the unit: -24.000000 is
not zero.
Unit Editor: Checking parameters for unit 'toto'.
Unit Editor: Checking for bond parameters.
Unit Editor: Checking for angle parameters.
Unit Editor: check: Warnings: 1
Unit Editor: Unit is OK.
> addions toto IB 0
24 IB ions required to neutralize.
Adding 24 counter ions to "toto" using 1A grid
Total solute charge: -24.00 Max atom radius: 2.10
Grid extends from solute vdw + 5.00 to 11.10
Box:
   enclosing: -34.53 -28.11 -26.32 23.77 28.80 27.11
   sized: 29.47 35.89 37.68
   edge: 64.00
Resolution: 1.00 Angstrom.
Tree depth: 6
grid build: 1 sec
Volume = 13.31% of box, grid points 34891
 (no solvent present)
Calculating grid charges
charges: 2 sec
Placed IB in toto at (-5.53, -0.11, -3.32).
Placed IB in toto at (-11.53, 6.89, 2.68).
Placed IB in toto at (1.47, 1.89, 15.68).
Placed IB in toto at (-7.53, -13.11, -8.32).
Placed IB in toto at (-15.53, 7.89, 12.68).
Placed IB in toto at (0.47, -2.11, -11.32).
Placed IB in toto at (-7.53, 9.89, -7.32).
Placed IB in toto at (-12.53, -21.11, -4.32).
Placed IB in toto at (11.47, 0.89, 16.68).
Placed IB in toto at (-15.53, -2.11, 15.68).
Placed IB in toto at (-17.53, -11.11, 9.68).
Placed IB in toto at (2.47, 9.89, -9.32).
Placed IB in toto at (10.47, 1.89, -7.32).
Placed IB in toto at (-7.53, -7.11, 19.68).
Placed IB in toto at (2.47, -9.11, 19.68).
Placed IB in toto at (0.47, -15.11, 9.68).
Placed IB in toto at (-7.53, -21.11, 5.68).
Placed IB in toto at (0.47, -21.11, -2.32).
Placed IB in toto at (8.47, -13.11, -5.32).
Placed IB in toto at (12.47, -7.11, 2.68).
Placed IB in toto at (18.47, 0.89, 6.68).
Placed IB in toto at (-21.53, -19.11, -9.32).
Placed IB in toto at (-27.53, -15.11, -2.32).
Placed IB in toto at (-25.53, -5.11, -0.32).

Done adding ions.
> saveamberparm toto GApU_duplex_ib.prmtop GApU_duplex_ib.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 150 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
 (no restraints)
> quit
        Quit

-------------------------------------------------------------

> Hi Tormod,
>
> I was looking over your email and noticed that according to the partial
> leap.log file you included, you are loading parm99.dat and are using
> amber6. According to the amber6 release, parm99.dat does not exist.
> There are parm98.dat, parm96.dat, parm94.dat, parm91X.dat, and
> parm91.dat, but no parm99.dat. Are you using a modified version or did
> you change the name of one of the parm*.dat files? Leap should have
> complained and not written out a prmtop file. Did you check to see
> where the IB ions were added in the structure (I.E. edit toto). Please
> send the entire leap.log file so we can track down the problem.
>
>
> Thanks,
>
> Rhonda
>
>
> On Tue, 30 Mar 2004, Skauge Tormod wrote:
>
> > Hi amber users,
> >
> > I'm trying to run a simulation of a RNA in vacuum. As recommended in the
> > amber DNA tutorial, I want to include a larger and softer counterion
> > than Na+ and have tried K+ and IB. Running sander for the heating
> > process (to 300K) fails with the comment "bad atom symbol: I" or "bad
> > atom symbol: K". According to ions94.lib, the definitions seem to be
> > correct. Any help on the matter is greatly appreciated (details below).
> >
> > thanks,
> > Tormod Skauge
> >
> >
> > Details:
> >
> > The counterions were added in xleap with:
> > > addions toto IB 0
> > input files generated with saveamberparm:
> > > saveamberparm toto GApU_duplex_ib.prmtop GApU_duplex_ib.inpcrd
> > The counterions are placed correctly and labelled "IB" or "K+" in the
> > prmtop file. Running sander (amber6):
> > $ sander -O -i testrun -o GApU_duplex_he_ib.out -c GApU_duplex_ib.inpcrd
> > -ref GApU_duplex_ib.inpcrd -p GApU_duplex_ib.prmtop -r
> > GApU_duplex_he_ib.rst
> > bad atom symbol: I
> >
> > I'm using parm99 and both parm99.dat and ions94.lib are loaded in xleap
> > (from leap.log):
> > Loading parameters: /usr/local/amber6/dat/parm99.dat
> > Loading library: /usr/local/amber6/dat/leap/lib/all_nucleic94.lib
> > Loading library: /usr/local/amber6/dat/leap/lib/all_amino94.lib
> > Loading library: /usr/local/amber6/dat/leap/lib/all_aminoct94.lib
> > Loading library: /usr/local/amber6/dat/leap/lib/all_aminont94.lib
> > Loading library: /usr/local/amber6/dat/leap/lib/ions94.lib
> >
> > The "testrun" file:
> > test to see if IB and K+ works
> >
> > &cntrl
> > IMIN=0, NTX=1, IREST=0, NSNB=99999,
> > TIMLIM=300, IG=71277, IBELLY=0,
> > IGB=1, NTB=0, GBPARM=2, GBSA=0,
> > DIELC=1, CUT=12.0, SCNB=2.0, SCEE=1.2,
> > NSTLIM=40000, DT=0.001,
> > HEAT=0.0, NTT=1, DTEMP=0.5, TAUTP=0.8,
> > NTC=2, TOL=0.0005, NTF=2,
> > NTPR=200, NTWX=500,
> > NMROPT=1, NTR=1,
> > &end
> > #Chauffage de 0 a 300 K
> > &wt TYPE='TEMP0', ISTEP1=0, ISTEP2=40000, VALUE1=0.0, VALUE2=300.0, &end
> > &wt TYPE='END', &end
> > &rst iat=0, &end
> > Group input for restrained atoms
> > 5.0
> > RES 1 99
> > END
> > END
> > &cntrl
> > imin = 0, ntb = 0,
> > igb = 1, ntpr = 500, ntwx = 500,
> > ntt = 1,
> > tempi = 300.0, temp0 = 300.0
> > nstlim = 5000, dt = 0.01,
> > cut = 12.0
> > &end
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
> -----------------------------------------------------------------------
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