[gmx-users] grompp or parameter file problem?

[Yang Ye]

set -pp for grompp and check processed top and find out why.

On 6/21/2007 6:09 PM, Anna Reymer wrote:
> 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>