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

[sharada]

Dear Gramacs users,
I am trying to simulate a peptide in Methanol. I am using Methanol216.gro file for the solvent. I could create the proper top and gro files of the peptide with the methanol solvent. However at the genbox step it says Number of solvent molecules =0
but when I open the final .gro file it has solvent molecules.  Whereas the .top file does not contain the solvent molecules. 
I am inserting the  output of genbox and .gro file for information.  
genbox -cp agg2box.gro -cs methanol216.gro -o agg2_b4em.gro -p agg2.top
Reading solute configuration
GROwing Monsters And Cloning Shrimps
Containing 71 atoms in 6 residues
Initialising van der waals distances...
Reading solvent configuration
"Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001"
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
   MeOH (   3 atoms):  1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 3042 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Neighborsearching with a cut-off of 0.45
Grid: 14 x 15 x 13 cells
Succesfully made neighbourlist
nri = 9007, nrj = 188363
Checking Protein-Solvent overlap: tested 693 pairs, removed 63 atoms.
Checking Solvent-Solvent overlap: tested 11134 pairs, removed 513 atoms.
Added 522 molecules
Generated solvent containing 1566 atoms in 522 residues
Writing generated configuration to agg2_b4em.gro
Back Off! I just backed up agg2_b4em.gro to ./#agg2_b4em.gro.1#
GROwing Monsters And Cloning Shrimps
Output configuration contains 1637 atoms in 528 residues
Volume                 :     35.0595 (nm^3)
Density                :     752.963 (g/l)
Number of SOL molecules:      0
Processing topology
Back Off! I just backed up agg2.top to ./#agg2.top.1#
-----------------------------------------------------------------------------------------------------------------------------
agg2_b4em.gro file reads like this......
GROwing Monsters And Cloning Shrimps
 1637
    1VAL      N    1   0.990   1.146   1.482
    1VAL     H1    2   0.961   1.053   1.507
    1VAL     H2    3   0.926   1.212   1.519
    1VAL     H3    4   0.994   1.154   1.382
    1VAL     CA    5   1.126   1.172   1.539
    1VAL     CB    6   1.229   1.061   1.497
    1VAL    CG1    7   1.372   1.085   1.552
    1VAL    CG2    8   1.189   0.918   1.542
    1VAL      C    9   1.170   1.317   1.498
    1VAL      O   10   1.202   1.344   1.382
    2GLN      N   11   1.175   1.411   1.595
    2GLN      H   12   1.145   1.386   1.687
    2GLN     CA   13   1.223   1.549   1.570
    2GLN     CB   14   1.153   1.643   1.673
    2GLN     CG   15   1.175   1.794   1.647
    2GLN     CD   16   1.115   1.887   1.752
    2GLN    OE1   17   1.180   1.929   1.847
    2GLN    NE2   18   0.990   1.924   1.740
    2GLN   HE21   19   0.936   1.892   1.662
    2GLN   HE22   20   0.949   1.985   1.808
    2GLN      C   21   1.379   1.558   1.572
---------
----------
- -------
 526MeOH   Me1 1629   2.760   3.368   2.738
  526MeOH    O2 1630   2.695   3.423   2.632
  526MeOH    H3 1631   2.615   3.371   2.606
  527MeOH   Me1 1632   0.288   3.224   2.925
  527MeOH    O2 1633   0.194   3.156   2.996
  527MeOH    H3 1634   0.212   3.059   2.983
  528MeOH   Me1 1635   2.506   3.095   2.599
  528MeOH    O2 1636   2.457   3.218   2.567
  528MeOH    H3 1637   2.390   3.204   2.494
   3.30500   3.58500   2.95900
Why does it say there are no SOL molecules.  Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
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