[gmx-users] add ion SCN - in OPLS-aa ff

[Justin A. Lemkul]

nana gomez wrote:
> 
>   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-
>  > ----------------
> 

Step 1 - upgrade to a newer Gromacs version in case this is a bug that has been 
fixed.  Using version 4.5.3, I cannot reproduce your problem.  Additional 
comments below.

>  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
> 

There have been issues in the past with stability of 180-degree angles.  Virtual 
sites are a better approach.

> * 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
>  
> 

grompp will throw a few warnings here without rlist=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
> 

I don't know whether the line breaks are a consequence of pasting into an email 
or something else, but if this is what your topology looks like, it's almost 
certainly the source of your error.  The format must be adhered to, and the 
random line breaks will cause problems in interpretation of the contents.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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