[gmx-users] RE: add new residue in OPLS-aa ff

[nana gomez]

  Dear Justin and All

 Right now, I am trying to add new residue in OPLS-aa ff

 when I make the following grompp -f file.mdp -c file.gro -p file.top -o file

 I have the following error
> --------------------
> Program grompp, VERSION 4.5.2
> Source code file: toppush.c, line: 1071
> 
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1 (rather,
> atomnr = -89390831, while at->nr = 0)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors-
> ----------------
 These are my files


 0- file forcefiel.itp
 [ defaults ]
 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
 1               3               yes             0.5     0.5
 
 1- file.rtp

 ; Ion thiocyanate adiciionado
 [ SCN ]
 [ atoms ]
 SQ   opls_966    -0.750    1
 CQ   opls_967     0.490    1
 NQ   opls_968    -0.740    1
 [ bonds ]

 CQ   SQ
 CQ   NQ


 2- file.atp

 opls_966   32.06000  ; SQ (SCN-)
 opls_967   12.01100  ; CQ (SCN-)
 opls_968   14.00670  ; NQ (SCN-)


 3- file ffbonded.itp

 [ bondtypes ]
 ; i    j  func       b0          kb
 CQ     SQ       1    0.16700   284082.0    ; JChemPhys_2008_118_154504
 CQ     NQ       1    0.11900   122389e1   ; JChemPhys_2008_118_154504

 [ angletypes ]
 ;  i    j    k  func       th0       cth

 SQ   CQ    NQ   1    180.000   652.802  ;JChemPhys_2008_118_154504

 4- file ffnonbonded.itp
 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_966   SQ    16    32.06000    -0.750       A    3.55000e-01  1.04600e+00
 opls_967   CQ     6    12.01100     0.490       A    3.75000e-01  4.39320e-01
 opls_968   NQ     7    14.00670    -0.740       A    3.25000e-01  7.11280e-01


5. file minimization.mdp

 ; Minimization
 integrator      = steep
 emtol           = 1000.0
 emstep          = 0.01
 nsteps          = 50000
 dt              = 0.01
 ns_type         = grid
 pbc             = xyz
 ;Electrostatic
 coulombtype     = PME pme_order       = 4
 fourierspacing  = 0.12
 rcoulomb        = 0.9
 rvdw            = 0.9
 
 6. file .gro
 SCN THIOCYANATE ION
 3
 1SCN     SQ    1   1.720   1.647   1.785
 1SCN     CQ    2   1.640   1.651   1.631
 1SCN     NQ    3   1.590   1.653   1.534
 3.30000   3.30000   3.30000

 7 file.top

 [ moleculetype ] ; Name            nrexcl
 Ion                 3

 [ atoms ]
 ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    ch
 argeB      massB
 ; residue   1 SCN rtp SCN  q -1.0
 1   opls_966      1    SCN     SQ      1      -0.75      32.06   ; qtot -0.
 75
 2   opls_967      1    SCN     CQ      1       0.49     12.011   ; qtot -0.
 26
 3   opls_968      1    SCN     NQ      1      -0.74    14.0067   ; qtot -1

 [ bonds ]
 ;  ai    aj funct            c0            c1            c2            c3
 1     2     1
 2     3     1

 [ angles ]
 ;  ai    aj    ak funct            c0            c1            c2            c3
 1     2     3     1
 ; Include topology for ions
 #include "./modif.ff/ions.itp"

 [ system ]
 ; Name
 SCN THIOCYANATE ION

 [ molecules ]
 ; Compound        #mols
 Ion                 1


 Thanks,

Ana GomezStudent 		 	   		   		 	   		   		 	   		  
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