[gmx-users] using g87 (converted from ambconv) in g_density

Hwankyu Lee leehk at umich.edu
Mon Oct 3 19:09:30 CEST 2005

Dear Gromacs users,

I've converted amber trajectories to g87 trajectories to use analysis 
tools of GROMACS.
After I converted them, when I used g_density, it failed to measure 
density of water, giving an error of "segmentation fault".   I think 
that the solute is successfully converted, but there may be a problem 
of solvent (water) because when I used g_gyrate of solutes, I didn't 
have any problems, but when I used g_density of solute+solvent, it 
didn't measure water density properly  (When I measure the solute in 
g_density, I could do that without any problem).

What I did is that...
1) ambconv -at uns.old.prmtop -gt uns.top -rst uns.inpcrd -common test 
-gro uns.gro --> unsolvated system
2) ambconv -at sol.old.prmtop -gt sol.top -rst sol.inpcrd -common test 
-gro sol.gro ---> solvated system
3) Add "#include mytip3p.itp" and "#include myions.itp" after 
"fftest.itp" to uns.top .
4) Add "Cl-    12" and "WAT    19345" to uns.top.
5) editconf -f sol.gro -o edit.gro -bt octahedron -box 9.37 9.37 9.37
6) grompp -f **.mdp -c edit.gro -p uns.top -o md.tpr   ----> there  was 
  no error!
** All prmtop files are old format by using new2oldparm.

I also added Cl- into myions.itp and checked fftestnb.itp and 
mytip3p.itp files, and make sure that all the atomtypes are included.  
Also, atomtype names and atom names in mytip3p.itp match those in 
fftestnb.itp and edit.gro.

Could you give me some advice on these problems?
Thanks for your help in advance.


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