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 [ 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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