[gmx-users] grompp or parameter file problem?

[Anna Reymer]

Hi Yang!

DNA is called protein.
ffamber_tip3p.itp is ancluded in the topology file.
Initially, when I run pdb2gmx I use an option -water and specify it to 'tip3p'
Here are some excerpt from my top file:

beginning:
------------------
; Include forcefield parameters
#include "ffamber99.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1 amber99_25      1    DC5    H5T      1     0.4422      1.008
; qtot 0.4422
     2 amber99_43      1    DC5    O5'      2    -0.6318         16
; qtot -0.1896
     3 amber99_11      1    DC5    C5'      3    -0.0069      12.01
; qtot -0.1965
     4 amber99_19      1    DC5   H5'1      4     0.0754      1.008
; qtot -0.1211
     5 amber99_19      1    DC5   H5'2      5     0.0754      1.008
; qtot -0.0457
     ....................................
end
-------
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
DICKERSON DODECAMER in water

[ molecules ]
; Compound        #mols
Protein             1
SOL             10682
--------------


Thank you very much for your help!!!

regards
/anna

On 6/20/07, Yang Ye <leafyoung at yahoo.com> wrote:
>
> What's the name for DNA under [ moleculetype ] in your top file?
> Another question is: have you included ffamber_tip3p.itp?
>
> Probably you need to post excerpt of your topology here if you are not sure
> about your answers towards above two questions.
>
> Regards,
> Yang Ye
>
>
> ----- Original Message ----
> From: Anna Reymer <anna.reymer at gmail.com>
> To: gmx-users at gromacs.org
> Sent: Wednesday, June 20, 2007 10:57:28 PM
> Subject: [gmx-users] grompp or parameter file problem?
>
>
> Hello all!
>
> I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port.
> I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro.
> When running grompp:
>
> grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr
>
> with the following em.mdp:
> -------------------------------------
> ;       DNA energy minimization in water
> ;
> cpp             = /lib/cpp -traditional
> define          =
> include         = -I/***/share/gromacs/top/ffamber99.itp
> constraints     = none
> integrator      = cg
> nsteps          = 1000
> ;
> ;       ENERGY MINIZATION STUFF
> ;
> emtol           = 2000
> emstep          = 0.01
> nstcgsteep      = 100
> nstcomm         = 1
> ns_type         = grid
> rlist           = 1
> rcoulomb        = 1.0
> rvdw            = 1.0
> Tcoupl          = no
> Pcoupl          = no
> gen_vel         = no
>
> I get the fatal error message:
> Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 448
>
> Fatal error:
> number of coordinates in coordinate file (genbox.gro, 32804)
>           does not match topology (dick.top, 0)
> -------------------------------------------------------
> Top file has all includes and its tail looks:
>
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL             10682
> ---------------------------------------------------------
> Does somebody have similar problems? Has somebody solved them?
>
> I will appreciate any help!
>
> regards
> /anna
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