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

2009-09-21 Thread Gunnar Widtfeldt Reginsson
You were right Justin. I had to include the lines: #ifdef _FF_AMBER [ moleculetype ] ; molname nrexcl Na+1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 amber99_31 1 Na+ Na 1 1 22.98977

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

2009-09-20 Thread 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: t

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

2009-09-20 Thread Mark Abraham
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: top

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

2009-09-20 Thread Gunnar Widtfeldt Reginsson
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 s