[gmx-users] Methanol SOL :Number of solvent molecules = 0

Mark Abraham Mark.Abraham at anu.edu.au
Tue Dec 11 07:06:04 CET 2007

sharada wrote:
> Dear Dr. Justin A. Lemkul
> Thank you for your reply. I tried adding the line 'SOL 522 ' at the end 
> of the .top file
> but genbox is deleting the line.

It will also need to correspond to a " [ molecule ] " section named SOL 
and the residues in your gro file will need to be named SOL.

> ------------------------------------------------------------
> Output configuration contains 1076 atoms in 341 residues
> Volume : 24.1334 (nm^3)
> Density : 720.413 (g/l)
> Number of SOL molecules: 0
> Processing topology
> Removing line #480 'SOL 522' from topology file (agg2.top)
> -------------------------------------------------------------------------------------------
> Thankyou Dr. Xavier Periole for indicating that the bonds and angle 
> information does not match with the original Gromos distributed file.  I 
> am inserting methanol.itp file  which came with gromacs distribution.  I 
> downloaded the methanol216.gro.gz from gromacs site.  Should I change  
> the bond values in the itp file? But it still does not solve the problem 
> of 'SOL molecules'. Since .top file indicates "#include "spc.itp". So if 
> I change it to #methanol.itp"   it should work.

That might work, by achieving part of what I suggest above, but you'll 
still need to change names in the .itp and .gro.

> -----------------------------------------------
> [root at ccmb top]# more methanol.itp

Don't do daily work as root, unless you like pain.


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