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From: lily jin (lily1907_at_yahoo.com)
Date: Thu Mar 15 2007 - 16:33:48 CDT
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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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- Next message: L. Michel Espinoza-Fonseca: "Re: AutoPSF"
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