I would say they are expecting a little more detailed information.
Could you please post the history of commands you typed to make the PDB. It
would be very helpful as well to have both ptraj-generated and the original
PDBs, for comparison.
Another thing is that you can do this RMSD calculation in ptraj, avoiding
this way the VMD calculation. You just need to define your original PDB as
the reference and then perform the calculations. In this way, you can select
just a group of atoms (e.g. the backbone of a protein) and hopefully this
will overcome the problem you're facing on VMD by loading the entire
structure.
As Daniel pointed out, pdbs from experimental data usually come with missing
atoms, and VMD is not able to deal with different atom numbers in two
structures.
Here is an example about how to do the rmsd fit to a reference file in
ptraj:
trajin your_trajectory.mdcrd #input trajectory
center :1-10 mass origin #your mask, check the number of the residues
image origin center #centering the image
reference your_pdb.pdb -1
rms reference mass out rmsd.dat :1-10[mask] #here you can define a mask
for your script, to account for only the heavy atoms of your system.
Good luck!
On Mon, Sep 26, 2011 at 2:00 AM, fatahiya <fatahiyamohdtap.yahoo.com> wrote:
> hi,
> tq Mr. Daniel Roe
>
> I was using ptraj in order to generate the pdb file form mdcrd file. Very
> messy means the bonds appear stretched. so, may i know why it happens?
>
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: fatahiya <fatahiyamohdtap.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Thursday, 22 September 2011 7:42 PM
> Subject: Re: [AMBER] RMSD
>
> Hi,
>
> In order to help you out some more information is needed about exactly
> what you have done. What procedure did you use to generate the PDB
> file? What does "very messy" mean (i.e. do bonds appear stretched, in
> the wrong places, etc?).
>
> On Thu, Sep 22, 2011 at 2:13 AM, fatahiya <fatahiyamohdtap.yahoo.com>
> wrote:
> > structure that i was download form pdb web. The no. of atom for my model
> is 210, the no.of atom for reference is 203.
>
> This will certainly cause problems for both Amber and VMD RMSD
> functions; the number of atoms in your reference has to be the same as
> in your target structure (atom ordering must be the same as well).
> It's not unusual for PDB files to be missing some parts of a structure
> (like terminals residues in a protein for example), in which case you
> can just calculate the RMSD of the parts of the structure that
> overlap. However, without knowing anything more about your system it's
> difficult to make specific recommendations.
>
> -Dan
>
> > can anybody tell me how these problems occur and how i want to do the
> rmsd alignment?
> >
> >
> > -fatahiya-fatahiyamohdtap.yahoo.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Sep 26 2011 - 06:00:03 PDT
