[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

[Biswajit Gorai]

Dear Lemkul,

Thanks.

Can any one suggest how/where to get the correct .itp file for Guanidinium
Chloride?

Regards
Biswajit

On Tue, Mar 20, 2012 at 5:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Biswajit Gorai wrote:
>
>> Dear GROMACS users,
>>
>> I am beginner to GROMACS. I want to simulate my protein in different
>> concentrations of Guanidinium Chloride solution and collected the files (3M
>> & 5M box and .itp file) from http://www.gromacs.org/**
>> Downloads/User_contributions/**Molecule_topologies<http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies>.
>> Then I build a topology file 'topol.top' (to minimize the box further) as
>>
>> ; Include forcefield parameters
>> #include "gromos43a1.ff/forcefield.itp"
>>
>> #include "gnd.itp"
>>
>> ; Include water topology
>> #include "gromos43a1.ff/spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>   1    1      1000       1000       1000
>> #endif
>>
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Gdm 3M
>>
>> [ molecules ]
>> ; Compound        #mols
>> GND 19
>> SOL             269
>> CL-             19
>>
>> Then I execute the command
>> $ grompp -f minim.mdp -c gnd3M.gro -p topol.top -o em.tpr
>>
>> But I got the following error
>>
>> Program grompp, VERSION 4.5.5
>> Source code file: toppush.c, line: 1631
>>
>> Fatal error:
>> Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> ------------------------------**-------------------------
>>
>> Is there something wrong with the .itp file (given) or I am doing any
>> mistake?
>>
>>
> The .itp file is wrong.  With pair type 2, 5 parameters are required
> (FudgeQQ, qi, qj, V, and W), unlike pair type 1, which only requires 2 (V
> and W).  See Table 5.5 in the manual for the required format.
>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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