VMD-L Mailing List

From: Rangeen Othman (rangeen.othman_at_googlemail.com)
Date: Wed Nov 26 2014 - 12:15:03 CST

Now I have the structure ( Gold atoms + lipid bilayer+ water) I want to
delete some water around gold nanoparticle to avoid clashes between atoms!
I have done it with just scripts as you have advised me but when I rewrite
the pdb and psf after deleting waters the coordinates of gold nano
particles are zero!
For example the final pdb like that til the end:
ATOM 54852 OH2 TIP3W9241 -2.899 1.217 27.357 1.00 0.00
 WT10 O
ATOM 54853 H1 TIP3W9241 -3.556 0.518 27.619 1.00 0.00
 WT10 H
ATOM 54854 H2 TIP3W9241 -2.067 0.714 27.395 1.00 0.00
 WT10 H
ATOM 54855 OH2 TIP3W9250 -6.839 1.532 33.356 1.00 0.00
 WT10 O
ATOM 54856 H1 TIP3W9250 -7.394 2.000 32.730 1.00 0.00
 WT10 H
ATOM 54857 H2 TIP3W9250 -5.922 1.685 32.999 1.00 0.00
 WT10 H
ATOM 54858 Au0 Au 1 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54859 Au1 Au 2 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54860 Au2 Au 3 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54861 Au3 Au 4 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54862 Au4 Au 5 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54863 Au5 Au 6 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54864 Au6 Au 7 0.000 0.000 0.000 -1.00 0.00 A

ATOM 54865 Au7 Au 8 0.000 0.000 0.000 -1.00 0.00 A

Thanks
Rangeen

On Wed, Nov 26, 2014 at 5:25 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Nov 26, 2014 at 12:09 PM, Rangeen Othman
> <rangeen.othman_at_googlemail.com> wrote:
> > Thanks for the reply, I want to merge both structures but it complained
> > about failed set of coordinates For example; "psfgen) Warning: failed to
> set
> > coordinate for atom AU31 AU:319 A". I have also used "
> > vmd>>extensions>>modeling>>merge structures " again gives me the same
> > warning! I have checked the merged pdb all coordinates of Au atoms are
> (0,
> > 0, 0)! I have used also topotools it worked and combined them, however,
> when
> > I wanted to delete some water around gold nanoparticle it failed again
> > because of using psfgen to do that!
>
> a) there is still not enough information here to see exactly what you
> have been doing.
> b) there is no need to use psfgen to remove some water, simple VMD
> scripting can do that.
>
>
> >
> > Thanks a lot
> >
> > Rangeen
> >
> > On Wed, Nov 26, 2014 at 4:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Wed, Nov 26, 2014 at 10:36 AM, Rangeen Othman
> >> <rangeen.othman_at_googlemail.com> wrote:
> >> > Dear VMD Users,
> >> >
> >> > I have two structures (gold nano particle with lipid bilayer, pdb and
> >> > psf
> >> > files) I want to combine them using Psfgen but it failed! I wonder if
> >> > someone will advise me what is the problem. Also I have checked that
> the
> >> > system has unique {segname resid name}. I have also used Topotool to
> >> > merge
> >> > them but again it failed and complained with the same phrase!
> >>
> >> there is not enough information here to give any advice, and i
> >> seriously doubt that psfgen and topotools give the same error message
> >> since they are completely different packages that don't share any
> >> code.
> >>
> >> axel.
> >>
> >>
> >> >
> >> > psfgen) reading coordinates from pdb file
> >> > mergetmp1312235701/2nmfix2.1s.pdb
> >> > psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A
> >> > psfgen) Warning: failed to set coordinate for atom AU1 AU:2 A
> >> > psfgen) Warning: failed to set coordinate for atom AU2 AU:3 A
> >> > psfgen) Warning: failed to set coordinate for atom AU3 AU:4 A
> >> > psfgen) Warning: failed to set coordinate for atom AU4 AU:5 A
> >> > psfgen) Warning: failed to set coordinate for atom AU5 AU:6 A
> >> > psfgen) Warning: failed to set coordinate for atom AU6 AU:7 A
> >> > psfgen) Warning: failed to set coordinate for atom AU7 AU:8 A
> >> > psfgen) Warning: failed to set coordinate for atom AU8 AU:9 A
> >> > psfgen) Warning: failed to set coordinate for atom AU9 AU:10 A
> >> > psfgen) Warning: failed to set coordinate for atom AU10 AU:11 A
> >> > psfgen) Warning: failed to set coordinate for atom AU11 AU:12 A
> >> > psfgen) Warning: failed to set coordinate for atom AU12 AU:13 A
> >> > psfgen) Warning: failed to set coordinate for atom AU13 AU:14 A
> >> > psfgen) Warning: failed to set coordinate for atom AU14 AU:15 A
> >> > psfgen) Warning: failed to set coordinate for atom AU15 AU:16 A
> >> > psfgen) Warning: failed to set coordinate for atom AU16 AU:17 A
> >> > psfgen) Warning: failed to set coordinate for atom AU17 AU:18 A
> >> > psfgen) Warning: failed to set coordinate for atom AU18 AU:19 A
> >> > psfgen) Warning: failed to set coordinate for atom AU19 AU:20 A
> >> >
> >> > Thanks in advance
> >> >
> >> > Rangeen
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>