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

[Justin A. Lemkul]

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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