[gmx-users] Problem with grompp , ffamber99 and ions

[Gunnar Widtfeldt Reginsson]

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 <jalemkul at 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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