VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Aug 28 2003 - 20:10:53 CDT

Hi John,

I've looked at the coordinates in the PDB file before loading it into
amber and after generating the pdb file in amber and they look different.
However I did not do a separate CM/CG calculation, I will do that and let
you know.

Thanks,
Ioana

On Thu, 28 Aug 2003, John Stone wrote:

>
> Ioana,
> Have you verified that the atom coordinates in the actual PDB file
> are correct? I suspect that the "centering" you're doing in Amber may
> not be affecting the coordinates as they are written out in the actual
> PDB file. It should be very easy for you to verify this by finding the
> atom(s) of interest in your PDB file in a simple text editor. The coordinates
> VMD uses are verbatim what it reads in from the PDB file, so I suspect that
> Amber is not actually writing out the transformed atom coordinates.
> Perhaps I'm missing something about the actual operations you're
> performing, but if you're just comparing coordinates between structures,
> I'd be quite surprised if VMD is doing something wrong there.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 28, 2003 at 03:55:35PM -0700, Ioana Cozmuta wrote:
> > Hi John,
> >
> > Thanks for your reply. I am not doing anything at all in VMD other than
> > loading the pdb structure, selecting atoms, calculating the center and
> > printing out the coordinates of the center. For such a structure
> > previously centered in zero in amber, vmd gives a non zero value for the
> > center (40A at least shifted).
> >
> > I found a way around this but I was just curious why the difference??
> > I will send you some example files after the 9th of September, I have a
> > deadline for that week as well...
> >
> > If you have any time to help me with the question I've submited about the
> > forces I would appreciate that a lot!
> >
> > Thanks and have a nice trip,
> > Ioana
> >
> > On Thu, 28 Aug 2003, John Stone wrote:
> >
> > >
> > > Ioana,
> > > Without the actual files to look at, its very hard for me to guess
> > > why you might be having the problem you describe. VMD loads structures
> > > in the same world coordinate system, so unless you've done various
> > > manipulations on one of the structures with some of the others toggled
> > > as "Fixed" in the main VMD windows, I can't think of a reason that
> > > they wouldn't retain exactly the same relative orientations and positioning
> > > (thus centering) that you had external to VMD. To eliminate any possible
> > > issues with temporary "fixing" followed by scaling/rotation/translation,
> > > make sure to do a Display->Reset View if they aren't lining up properly.
> > > This undoes any inadvertent molecule-specific viewing transformations
> > > you may have caused by using the "Fixed" toggle in the main VMD window.
> > >
> > > If this doesn't solve your problem, please email us some example files,
> > > and I'll help you solve your problem when I return from being out of town.
> > > I'll be out until September 9th, so it'll be a while, but if you post
> > > to VMD-L, perhaps someone else can help solve your problem while I'm away.
> > >
> > > Thanks,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Mon, Aug 25, 2003 at 05:29:55PM -0700, Ioana Cozmuta wrote:
> > > > Hi John,
> > > >
> > > > What I am actually tying to do is the following:
> > > > I have to structures: a protein and a box with water.
> > > > I want to center them in zero, align them with the z axis and remove
> > > > all the atoms from the box that overlap with the protein.
> > > > The problem is the following: if I center both structures in amber (tleap)
> > > > in zero when I view them in VMD their centers do not overlap and also
> > > > their centers is not zero anymore (although I've especially done that in
> > > > amber).
> > > > I am just curious why this difference? I wrote a code that does the
> > > > removal of the overlaping molecules, that's what I need the radii for.
> > > > I will add there the centering but then again I might want to vizualize
> > > > the centered structure and vmd may show them again shifted from each
> > > > other...
> > > >
> > > > Thanks,
> > > > Ioana
> > > >
> > > > On Mon, 25 Aug 2003, John Stone wrote:
> > > >
> > > > > Dear Ioana,
> > > > > VMD reads and interprets only the PDB columns it knows how
> > > > > to make use of. As such, when writing out PDB files from VMD,
> > > > > some of the columns get default values, or are left blank,
> > > > > particularly for fields that VMD doesn't store. According to
> > > > > the PDB file spec, the last two fields of the ATOM recard
> > > > > are supposed to contain the element symbol (cols 77-78) and
> > > > > the charge (cols 79-80). Which actual fields/columns are you
> > > > > storing the radii and charge in?
> > > > >
> > > > > In any case, I suspect that there's no easy way for you to preserve
> > > > > the custom radii/charge info unless you were to store it in the
> > > > > occupancy and tempFactor fields, which VMD does actualy store and
> > > > > should also save.
> > > > >
> > > > > Since VMD isn't intended specifically to work with just PDB files,
> > > > > there are many PDB record types and fields that VMD doesn't process,
> > > > > so this is only one example of all kinds of similar limitations with PDB
> > > > > and potentially with other formats,
> > > > >
> > > > > Thanks,
> > > > > John Stone
> > > > > vmd_at_ks.uiuc.edu
> > > > >
> > > > > On Mon, Aug 25, 2003 at 04:24:27PM -0700, Ioana Cozmuta wrote:
> > > > > > Hi vmd users,
> > > > > >
> > > > > > I am reading in VMD a pdb file and in the last two columns of the file I
> > > > > > have the charge and radii. However after I recenter the structure and
> > > > > > select all atoms, when I write the selection into a pdb file the last two
> > > > > > columns loose the information. Is there a way to preserve the charge/radii
> > > > > > information when I write the atomselection into the pdb file?
> > > > > >
> > > > > > Thank you,
> > > > > > Ioana
> > > > >
> > > > > --
> > > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > > Beckman Institute for Advanced Science and Technology
> > > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > > > >
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>