VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Nov 26 2014 - 17:02:34 CST

Hi Rangeen,

I see you have been making more posts. I live in a different time zone
compared to you - so you need to be a bit patient when you ask someone for
help.

I have explained to you on a number of occasions that your system in not
conventional, and you are not trying to understand it.

Since, in the files you sent me you conveniently didn't add the topology
and parameter files that define your GOLD nanoparticle, I had to look up
the topology/parameter info for gold. When I looked it up just now I
couldn't even find it (I admit that I spent just 3-4 minutes on it).

I will repeat again, hopefully for the last time - you have bonds between
your gold atoms, I don't know if gold has bonds between atoms, but clearly
the psf of the nanoparticles shows it has. You must have built that PSF
(for the gold nanoparticle) using some topology file. You need to PASS that
topology to psfgen which it will append to lipid's topology that you have
already had it read.

what that means is you need to add the following line after you call the
psfgen package:

topology (topology_of_gold_nanoparticle.extention)
** Do not include the brackets and replaces the contents of the bracket
with the name of the topology file.

I am not sure if psfgen reads the prot_na_lipid topology by default ???
from the error you sent me earlier maybe it does - you need to check that.

The only cause of your error is that you are not giving the topology
definitions to psfgen, other merging psf/pdb is just a standard -
READ/MERGE/WRITE operation.

I will also repeat again - that you need to understand two things:

What is your system?
What are the preparatory steps of preprocessing before you can run the MD?

After that you ALSO need to understand how MD works but for now focus on
these. If you spend a couple of days on this - you will be far better off
then wasting many days in explaining to others what your problem is and
waiting for them to find time to look at your problem ( I do apologize for
replying late).

If in all this if you forgot what I said, here it is again:

give psfgen the topology of your nanoparticle.

I hope this will solve your problem.

Best,
/A

On Thu, Nov 27, 2014 at 10:50 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Nov 26, 2014 at 4:32 PM, Rangeen Othman
> <rangeen.othman_at_googlemail.com> wrote:
> > Ok sorry for that. First, I have built a gold nanoparticle with
> inorganic builder using VMD. So I have pdb and psf for it but there is no
> bonds, angels and etc in the psf file. Second I have used inorganic
> builder to add bonds and topotool to make angles. So if you are following
> me now I have psf and pdb for the gold nanoparticle. Third I have the pdb
> and psf for membrane in a box of water, I have loaded both structures into
> VMD, then move the gold nanoparricle into the position I wanted and saved
> that coordinates. Then loaded the final structure of goldnanoparticle into
> VMD. Finally, tried to combine them together using Topotool and it worked.
> The problem is deleting water around the gold atoms! I have used simple
> scripts to delete waters but when I havd rewritten that into the pdb and
> psf the coordinates of gold nanoparticle are became zero which is unusual!
> > I hope you understand me now.
>
> i *did* understand you, but you don't understand me. it *still*
> doesn't help because you only *describe* what you have been doing (or
> think you have been doing). how can we know whether you did it
> correctly? and what you did in particular? any description that is
> qualified with "it worked" or "it didn't work" is not very helpful.
>
> obviously your "simple scripts" are broken. i never had this problem
> with this kind of procedure. there is a commented example script on my
> homepage at:
>
>
> https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal
>
>
> > Thanks
> > Rangeen
> >
> >
> > Sent from my iPhone
> >
> >> On 26 Nov 2014, at 18:33, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >>
> >> On Wed, Nov 26, 2014 at 1:15 PM, Rangeen Othman
> >> <rangeen.othman_at_googlemail.com> wrote:
> >>> 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!
> >>
> >> let me repeat. nobody can give advice, when you don't give details. my
> >> only conclusion is that you didn't do what you said you are doing
> >> correctly. atom coordinates are only set to zero when either: you have
> >> an incorrectly formatted pdb file or: you ask psfgen to regenerate
> >> coordinates without providing a suitable topology file. neither case
> >> should happen, if you are using topotools and VMD correctly.
> >>
> >> axel.
> >>
> >>
> >>> 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.
> >>
> >>
> >>
> >> --
> >> 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.
>
> 

-- 
Best,
/A