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

[Justin A. Lemkul]

Quoting sharada <sharada at ccmb.res.in>:

> 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
>

My guess would be that it is because there are no molecules named SOL in your
output.  Gromacs uses SOL for water, and since your system lacks water, genbox
is accurately telling you there are no "SOL" within the output.

Note the line above where genbox is telling you that it added 522 molecules, and
add this information into your .top file.

-Justin


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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