You were right Justin. I had to include the lines:
#ifdef _FF_AMBER
[ moleculetype ]
; molname nrexcl
Na+ 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
mass
1 amber99_31 1 Na+ Na 1 1
22.98977
#endif
int the ions.itp
And there were no errors
Thanks again.
On Sun, Sep 20, 2009 at 11:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
>
>
> Gunnar Widtfeldt Reginsson wrote:
>
>> Hi.
>> I am trying to run this command on a solvated DNA
>>
>> grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx
>>
>> and I get this fatal error:
>> -------------------------------------------------------
>> Program grompp, VERSION 4.0.5
>> Source code file: toppush.c, line: 1641
>>
>> Fatal error:
>> No such moleculetype Na+
>> -------------------------------------------------------
>>
>> I have added to the file ions.itp :
>> [ moleculetype ]
>> ; molname nrexcl
>> Na+ 1
>>
>> [ atoms ]
>> ; id at type res nr residu name at name cg nr charge
>> 1 amber99_31 1 Na+ Na 1 1
>>
>>
> Is this section contained in an appropriate #ifdef _FF_AMBER block?
>
> -Justin
>
>
>> because this is how the Na ion is in ffamber99.rtp
>>
>>
>> [ Na+ ]
>> [ atoms ]
>> Na amber99_31 1.00000 1
>>
>> And this I have done according to the amber website:
>> http://chemistry.csulb.edu/ffamber/#aadat
>>
>>
>> The last part of the topol.top file is:
>> SOL 13651
>> Na+ 38
>> Cl 0
>>
>> and the structure file contains:
>> ATOM 55905 Na Na+ 3729 77.070 47.215 21.822 1.00 0.00
>>
>> Does anyone know what could be wrong?
>>
>> Thanks.
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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