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
because this is how the Na ion is in ffamber99.rtp
Did you do
#include "ions.itp"
?
Mark
[ 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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