VMD-L Mailing List

From: fan li (fanliqmul_at_gmail.com)
Date: Wed May 16 2018 - 16:56:21 CDT

Hi

I did manage to add water molecules, but unphysical bonds are still there.

There is a atom at the origin, and lots of strange bonds are connected to
it ,but it was there before I add water molecules because it is part of
molecule2.

Moreover, I am using Josh's script to reorder my structure (with water) in
the post http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/29671.html

and the convert to .top file. I found that the final top lists molecules in
the following way see below

#############################
[ system ]
; Name
vmdmolecule3

[ molecules ]
; Compound #mols
molecule0 1
molecule1 1
molecule2 1380
molecule3 1
molecule4 10
molecule5 1
molecule6 2370
molecule7 1
molecule8 10
molecule9 1
molecule10 1191
molecule11 472
########################
It looks weird because molecules who have number larger than 1 are all
water molecules,so the structure seems to be separated by water.

Then I modified the script a little bit
#########################################
topo cleardihedrals

#sort the structure and abandon the repeated fragments
set fragsellist [list ]
set asel [atomselect top "not type Kp or resname TIP3"]

foreach frag [lsort -unique [$asel get fragment]] {
set fsel [atomselect top "fragment $frag"]
lappend fragsellist $fsel
}

set midsel [atomselect top "resname TIP3"]
lappend fragsellist $midsel

#append K+ at the end of the pdb and psf files
set potsel [atomselect top "type Kp"]
$potsel set name K
lappend fragsellist $potsel
set newmol [::TopoTools::selections2mol $fragsellist]

pbc set [list $xmax $ymax $zmax]

animate write psf AFM_reordered.psf $newmol
animate write pdb AFM_reordered.pdb $newmol

topo writegmxtop AFM_reordered.top [list **.prm]
##########################################################

the results are more weird ,see below.
#############################################
[ system ]
; Name
vmdmolecule3

[ molecules ]
; Compound #mols
molecule0 1
molecule1 1
molecule2 1380
molecule3 1
molecule4 10
molecule5 1
molecule6 2370
molecule7 1
molecule8 10
molecule9 1
molecule10 6152
molecule11 472
#################################################

Can someone tell me what is wrong?

Thanks a lot.

Fan

2018-05-16 2:23 GMT+01:00 Dallas Warren <dallas.warren_at_monash.edu>:

> Can't help with the first 1/ 2/, however with 3/ vmd generates bonds
> to display based on the distance that the molecules are apart, not due
> to any bonds present within a topology.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren_at_monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 16 May 2018 at 07:59, fan li <fanliqmul_at_gmail.com> wrote:
> > Hi every one
> >
> > I have molecule1 in the middle of my box, and molecule2 at the bottom.
> Now I
> > want to fill the other volume not occupied by molecule1 and molecule2. I
> > tried following command
> >
> > solvate ubq.psf ubq.pdb -t 5 -o ubq_wb
> >
> > It created the water around the molecule1 and molecule2, but the
> molecule2
> > is already at the boundary of my box,so there should be no waters below
> it.
> >
> > (1)How can I fill the other volume not occupied by molecule1 and
> molecule2
> > in vmd?
> >
> > (2)And what is the density of the solvate?
> >
> > (3)I also noticed that my original psf might be changed after I used the
> >
> > solvate ubq.psf ubq.pdb -t 5 -o ubq_wb because some non-physical bonds is
> > generated in the display window? Why it happend?
> >
> > Fan
>
>