VMD-L Mailing List

From: lily jin (lily1907_at_yahoo.com)
Date: Thu Mar 15 2007 - 17:02:37 CDT

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* > > > > > > > ------------------------------------------------------------------------ > > > No need to miss a message. Get email on-the-go > > > > <http://us.rd.yahoo.com/evt=43910/*http://mobile.yahoo.com/mail> > > > with Yahoo! Mail for Mobile. Get started. > > > > <http://us.rd.yahoo.com/evt=43910/*http://mobile.yahoo.com/mail> > > > > ________________________________ > Need Mail bonding? > Go to the Yahoo! Mail Q&A for great tips from Yahoo! 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