[gmx-users] methanol as a solvent

[Alok]

Hello,

         i was trying to solvate  speptide(given in tutotorial of gromacs)
by methanol in place of SPC .
         i did first two steps same as given in tutorial for speptide
(pdb2gmx,editconf).
     For genbox i only change the solvent input file. i specified
meoh_WFG.gro in place of spc216.gro (which is uploaded by "Christoph
Freudenberger" in gromacs topogies. thanks for it )

 genbox -cp out -cs meoh_WFG.gro -p speptide -o b4em

my problem is that solvent(methanol) is not  added  in speptide.top file.
can someone point out my mistake.
Thanks in advance.

i am attaching the output of genbox :-

Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/share/gromacs/top/atommass.dat
Opening library file /usr/local/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 191 atoms in 19 residues
Initialising van der waals distances...
Reading solvent configuration
"MeOH solvent box, 400 molecules, CF 13/03/03"
solvent configuration contains 1200 atoms in 400 residues

Initialising van der waals distances...
Will generate new solvent configuration of 1x2x1 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
   MeOH (   3 atoms):   800 residues
Calculating Overlap...
box_margin = 0.315
Removed 609 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 0 data points for COUL.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 2591 charge groups and 2591 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 12 x 19 x 10 cells
Succesfully made neighbourlist
nri = 4450, nrj = 50057
Checking Protein-Solvent overlap: tested 1864 pairs, removed 162 atoms.
Checking Solvent-Solvent overlap: tested 11554 pairs, removed 255 atoms.
Added 458 molecules
Generated solvent containing 1374 atoms in 458 residues
Writing generated configuration to b4em.gro
Go Rough, Oppose Many Angry Chinese Serial killers

Output configuration contains 1565 atoms in 477 residues
Volume                 :     34.9038 (nm^3)
Density                :     731.971 (g/l)
Number of SOL molecules:      0



                                           Alok jain
                                    Indian Institute of Tecnology
                                        Kanpur, India