VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Mar 15 2007 - 16:41:55 CDT

hm, this is weird. Apparently, the H's of the N-terminus group are not
being saved. Are you sure you included them in your original file? I
know this question might sound dumb, but it could happen. Could you
send the first lines of your ORIGINAL file, so we can check this small
detail?

Michel

2007/3/15, lily jin <lily1907_at_yahoo.com>:
>
>
>
> Peter and Micheal,
>
> Thank you for helping.
>
> As Peter said using pdb file I can solve visualization problem. Thank you.
>
>
>
> I can removed the ions as Micheal said. However, I have ATP and metals in
> the protein and I want to include them. I used "not water and not ion" still
> have different atom numbers. Is there another way?
>
>
>
> I looked up the pdb files saved directly by VMD and the one gerated from
> Autopsf. AutoPsf added some hydrogen atoms at the N end of each chain. As
> below:
>
>
>
> Original :
>
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>
> ATOM 1 N ASP A 24 160.883 64.782 53.437 1.00 0.00 A
>
> ATOM 2 HN ASP A 24 161.448 64.527 54.319 1.00 0.00 A
>
> ATOM 3 CA ASP A 24 159.743 63.991 53.130 1.00 0.00 A
>
> ATOM 4 HA ASP A 24 160.007 62.981 52.901 1.00 0.00 A
>
> ATOM 5 CB ASP A 24 158.920 64.094 54.463 1.00 0.00 A
>
> ATOM 6 HB1 ASP A 24 159.641 64.185 55.300 1.00 0.00 A
>
> ATOM 7 HB2 ASP A 24 158.297 65.010 54.503 1.00 0.00 A
>
>
>
> PSF generated:
>
> REMARK original generated coordinate pdb file
>
> ATOM 1 N ASP A 24 160.883 64.782 53.437 1.00 0.00 P1 N
>
> ATOM 2 HT1 ASP A 24 161.357 64.379 54.220 0.00 0.00 P1 H
>
> ATOM 3 HT2 ASP A 24 160.585 65.710 53.660 0.00 0.00 P1 H
>
> ATOM 4 HT3 ASP A 24 161.490 64.800 52.643 0.00 0.00 P1 H
>
> ATOM 5 CA ASP A 24 159.743 63.991 53.130 1.00 0.00 P1 C
>
> ATOM 6 HA ASP A 24 160.007 62.981 52.901 1.00 0.00 P1 H
>
> ATOM 7 CB ASP A 24 158.920 64.094 54.463 1.00 0.00 P1 C
>
> ATOM 8 HB1 ASP A 24 159.641 64.185 55.300 1.00 0.00 P1 H
>
> Lily
>
>
>
> ----- Original Message ----
> From: L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
> To: Peter Freddolino <petefred_at_ks.uiuc.edu>
> Cc: lily jin <lily1907_at_yahoo.com>; VMD-L <vmd-l_at_ks.uiuc.edu>
> Sent: Thursday, March 15, 2007 1:56:59 PM
> Subject: Re: vmd-l: AutoPSF
>
>
> Hi,
>
> In addition to what petter has said, perhaps you also saved the ions
> included in your system (I assume there are a few of them). You could
> try to select only the protein (for example, by using "atomselect top
> protein").
>
> Michel
>
> 2007/3/15, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> > Hi Lily,
> > autopsf will fill in any missing atoms in residues, so if you
> > accidentally cut out some solute atoms when removing the water, or are
> > missing termini, these will be added. If you send your files I can track
> > down the specific differences (you can probably do the same by looking
> > at what atoms are present only in one).
> > Are you planning to use this psf for visualization or energetic
> > analysis? If you only need it for visualization, you can just use a pdb
> > instead.
> >
> > Peter
> >
> > lily jin wrote:
> > > Hi,
> > > My protein was in a waterbox during simulation. I want to removed the
> > > waterbox when I analyze the results. I saved a dcd file without water.
> > > The atom number is 51353. Then I use AutoPSF plugin to generate a PSF
> > > file without water. However, the genrated PSF and PDB files include
> > > 51380 atoms. What makes the difference? What can I do to make them
> > > match? Thank you!
> > >
> > >
> > > *Lily*
> > >
> > >
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