[gmx-users] Methanol SOL :Number of solvent molecules = 0
Xavier Periole
X.Periole at rug.nl
Tue Dec 11 00:13:34 CET 2007
Note that topology of the methanol in the gromacs distribution does
not correspond to the original GROMOS methanol model. One distance
is changed and the original model does not have an angle discribing
CMET-OMET-H but a distance between CMET-H.
Anybody knows where the changes come from?
The bond topology of the original GROMOS model is as below.
[ bonds ]
; ai aj funct c0 c1
1 2 1 0.14300 376560.
2 3 1 0.10000 313800.
1 3 1 0.19880 313800.
XAvier.
On Mon, 10 Dec 2007 06:36:56 -0500
"Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 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
>
>
> ========================================
>
> 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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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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