From: lily jin (lily1907_at_yahoo.com)
Date: Thu Mar 15 2007 - 16:33:48 CDT

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> > ____________________________________________________________________________________ 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news