VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Mar 15 2007 - 17:13:38 CDT

Eureka! Lily, if you carefully look at the file you used for your
simulation and the file created by psfgen, you'll see that the three
hydrogens from the N-terminus are missing. If you check the topology
file, you'll see that they SHOULD be there:

PRES NTER 1.00 ! standard N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HT1
ATOM HT2 HC 0.33 ! (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT1 0.21 ! | \
ATOM HA HB 0.10 ! HA HT3
DELETE ATOM HN

This is the standard topology for the NH3+ terminus. As you can see,
what psfgen is doing is replacing the H(N) atom from the truncated
backbone by three new hydrogens. Try to check again your protein and
re-run your simulation.

Good luck!
Michel

2007/3/15, lily jin <lily1907_at_yahoo.com>:
>
>
>
> PDB file0: which I sent to NAMD, generated by psfgen. With a waterbox
>
> ----------------------------
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>
> ATOM 1 N ASP A 24 154.415 72.723 45.425 1.00 0.00 A
>
> ATOM 2 HN ASP A 24 155.223 72.503 45.935 1.00 0.00 A
>
> ATOM 3 CA ASP A 24 153.706 71.521 44.936 1.00 0.00 A
>
> ATOM 4 HA ASP A 24 154.289 71.071 44.152 1.00 0.00 A
>
> ATOM 5 CB ASP A 24 153.566 70.415 46.077 1.00 0.00 A
>
> ATOM 6 HB1 ASP A 24 152.849 69.639 45.762 1.00 0.00 A
>
> ATOM 7 HB2 ASP A 24 154.515 69.955 46.448 1.00 0.00 A
>
> ATOM 8 CG ASP A 24 152.910 71.015 47.315 1.00 0.00 A
>
> ATOM 9 OD1 ASP A 24 153.660 71.379 48.288 1.00 0.00 A
>
> ATOM 10 OD2 ASP A 24 151.631 71.100 47.389 1.00 0.00 A
>
> ATOM 11 C ASP A 24 152.467 71.873 44.162 1.00 0.00 A
>
> ATOM 12 O ASP A 24 152.457 72.124 42.930 1.00 0.00 A
>
> ATOM 13 N LEU A 25 151.346 71.943 44.843 1.00 0.00 A
>
> ATOM 14 HN LEU A 25 151.320 71.881 45.846 1.00 0.00 A
>
> -------
>
> After simulation, I opened the dcd and psf in VMD with waterbox.
>
> PDB file1: saved by VMD with 'not water'
>
> -----------------------------
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>
> ATOM 1 N ASP A 24 153.055 72.073 39.901 1.00 0.00 A
>
> ATOM 2 HN ASP A 24 152.492 72.775 39.446 1.00 0.00 A
>
> ATOM 3 CA ASP A 24 152.423 71.549 41.090 1.00 0.00 A
>
> ATOM 4 HA ASP A 24 152.789 70.549 41.076 1.00 0.00 A
>
> ATOM 5 CB ASP A 24 152.977 72.318 42.400 1.00 0.00 A
>
> ATOM 6 HB1 ASP A 24 152.400 71.974 43.247 1.00 0.00 A
>
> ATOM 7 HB2 ASP A 24 153.987 72.093 42.650 1.00 0.00 A
>
> ATOM 8 CG ASP A 24 152.840 73.783 42.344 1.00 0.00 A
>
> ATOM 9 OD1 ASP A 24 151.780 74.234 42.923 1.00 0.00 A
>
> ATOM 10 OD2 ASP A 24 153.707 74.512 41.812 1.00 0.00 A
>
> ATOM 11 C ASP A 24 150.935 71.579 40.871 1.00 0.00 A
>
> ATOM 12 O ASP A 24 150.439 71.211 39.779 1.00 0.00 A
>
> ATOM 13 N LEU A 25 150.097 72.076 41.848 1.00 0.00 A
>
> ATOM 14 HN LEU A 25 150.578 72.511 42.578 1.00 0.00 A
>
> --------
>
> PDB file2: generated by Autopsf plug in of VMD1.8.5 with "not water"
>
> 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
>
> ATOM 9 HB2 ASP A 24 158.297 65.010 54.503 1.00 0.00 P1 H
>
> ATOM 10 CG ASP A 24 158.109 62.825 54.707 1.00 0.00 P1 C
>
> ATOM 11 OD1 ASP A 24 157.195 62.539 53.874 1.00 0.00 P1 O
>
> ATOM 12 OD2 ASP A 24 158.375 62.164 55.732 1.00 0.00 P1 O
>
> ATOM 13 C ASP A 24 159.020 64.589 51.951 1.00 0.00 P1 C
>
> ATOM 14 O ASP A 24 159.552 65.302 51.046 1.00 0.00 P1 O
>
> ATOM 15 N LEU A 25 157.685 64.344 51.737 1.00 0.00 P1 N
>
> ATOM 16 HN LEU A 25 157.193 63.831 52.475 1.00 0.00 P1 H
>
> ATOM 17 CA LEU A 25 156.899 64.878 50.637 1.00 0.00 P1 C
>
> Lily
>
>
>
> ----- Original Message ----
> From: L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
> To: lily jin <lily1907_at_yahoo.com>
> Cc: Peter Freddolino <petefred_at_ks.uiuc.edu>; VMD-L <vmd-l_at_ks.uiuc.edu>
> Sent: Thursday, March 15, 2007 2:41:55 PM
> Subject: Re: vmd-l: AutoPSF
>
>
> 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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