VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Nov 27 2014 - 08:48:56 CST

Again, when you are here:

Then I have solvated a membrane and combined it with gold:
> set psf0 solvate.psf
> set pdb0 solvate.pdb
> set psf1 2nmfix2.psf
> set pdb1 2nmfix2.pdb
> set outName mem_gold1
> set finalPsf $outName.psf
> set finalPdb $outName.pdb
> package require psfgen
> resetpsf
> readpsf $psf0
> coordpdb $pdb0
> readpsf $psf1
> coordpdb $pdb1
> # Write the combination.
> writepdb $finalPdb
> writepsf $finalPsf

The PSF can't be written without a topology. You say later that:

So the structure is fine now.

That is only because you merged the two structures together.

> So in this stage again system_fixwat.pdb has zero coor for gold atoms!

Since you didn't solve this error before - it still exists.

I don't use topotools so I can not add more to this, but reading its manual
gives the impression that it *MAY* not serve your cause.

I am not sure what you mean by a lot of people have used it, it is a tool
so it was written for a purpose and obviously people would be using it,
however it in no way means that it would tend to your needs.

As I suggested to you in the very start you should read how other people
have simulated nano-particles or are doing now. Those publications will
have an accepted way of dealing with all of these things that you are
basically reinventing.

To start you on this (which I think you are not willing to do on your own)
here is a publication you need to read:

http://pubs.acs.org/doi/abs/10.1021/ct301018m?journalCode=jctcce

Also, as I explained before you need to think about formation of the
nano-particles (i.e. how they are arranged in space). The above paper talks
about where people have spent time devising a correct approach to do this.
You need to use something like the GoIP/GolP-CHARMM force field. It is
compatible with NAMD, so if you use that you will not have to use topotools
(to guess bonds). Should this not work, it would be easy (if you are doing
crude work) to manually put this together. If I were you I would use the
example of the fullerene's topology to get an idea and write my own.

A google search turned that up as an attachment here :
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/3883.html

Note that with fullerenes there are actual bonds between carbon atoms where
as in your case you are just putting them in (as I understand it) so that
they stick together (which is not very convincing) also note that once you
write your topology file - you need to have parameters for those bonds as
well, which would be used during the simulation.

I will leave you to this and hope you are able to resolve your problem
using this Force Field specifically designed for use with gold
nanoparticles or writting the topology and parameter file manually.

Good Luck.

Best,
/A

On Fri, Nov 28, 2014 at 1:29 AM, Rangeen Othman <
rangeen.othman_at_googlemail.com> wrote:

> Thanks a lot Alex and sorry again yes I haven't explained the procedure!
> I have used the following scripts to make a psf for gold.
> #mol new "Au_bond2.pdb" autobonds no waitfor all
> set atoms [atomselect top all]
> $atoms set type Au
> $atoms set segname A
>
> mol bondsrecalc top
> package require topotools
> topo retypebonds
> vmdcon -info "assigned[topo numbondtypes] bond types to [topo #numbonds]
> bonds;"
> vmdcon -info "bondtypes:[topo bondtypenames]"
> topo guessangles
> vmdcon -info "assigned[topo numangletypes] angle types to [topo
> numangles] angles;"
> vmdcon -info "angletypes:[topo angletypenames]"
> mol reanalyze top
> animate write pdb 2nmfix1.pdb
> animate write psf 2nmfix1.psf
>
> Then I have solvated a membrane and combined it with gold:
>
> set psf0 solvate.psf
> set pdb0 solvate.pdb
> set psf1 2nmfix2.psf
> set pdb1 2nmfix2.pdb
>
> set outName mem_gold1
>
> set finalPsf $outName.psf
> set finalPdb $outName.pdb
> package require psfgen
> resetpsf
> readpsf $psf0
> coordpdb $pdb0
> readpsf $psf1
> coordpdb $pdb1
>
> # Write the combination.
> writepdb $finalPdb
> writepsf $finalPsf
>
> It failed to read the set coordinates of Gold, so pdb has zero coor
> for gold however the psf was created for the system, so I have used
> this to read the coor of gold into the pdb;
> 1) remove "END" at the end of solvate.pdb
> 2) cat solvate.pdb 2nmfix2.pdb > mem_gold1.pdb
> 3) vmd mem_gold1.psf mem_gold1.pdb
>
> So the structure is fine now.
>
> Then wanted to delete unwanted water:
>
> mol load psf mem_gold1.psf pdb modelsystem.pdb
>
> set bad [atomselect top {same residue as \
> (water and within 2.9 of resname Au)or\
> (water and (x<-50 or x>28 or y<-50 or y>28))or\
> (water and abs(z)<18)}]
>
> resetpsf
> readpsf mem_gold1.psf
> coordpdb mem_gold1.pdb
> foreach segid [$bad get segid] resid [$bad get resid] name [$bad get name]
> {
> delatom $segid $resid $name
> }
> writepsf system_fixwat.psf
> writepdb system_fixwat.pdb
>
> So in this stage again system_fixwat.pdb has zero coor for gold atoms!
>
> Sorry Ashar I wasn't patient, and thanks alot you are totally right,
> but I haven't used a topology file to make a psf, instead of that I
> have used topotool to make a psf, I think it is not a problem to make
> psf with topotool. I have seen that so many people used topotool to do
> that and there was not a problem!
>
> Thanks all for advises and sorry again
>
> Rangeen
>
>
>
>
> Sent from my iPhone
>
> > On 26 Nov 2014, at 21:50, 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