From: lily jin (lily1907_at_yahoo.com)
Date: Thu Mar 15 2007 - 17:35:56 CDT

Gosh. The simulation started over two years ago by someone in the lab and he has left. It seems not possible to rerun the simulation. But hope it dosen't matter too much (just the ternimus). Doe it matter much? I am glad to see the mistake there. But I doubt why? We always use the psfgen.exe (not sure where it came from) and the top_all27_pro_na.inp to generate psf. I checked some another pdb file that I generated using the same method. The structure dosen't have the three Hydrogen itoms either. But the topology file dose have them as in your email. 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 3:13:38 PM Subject: Re: vmd-l: AutoPSF 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* > > > > > > > > > > > ------------------------------------------------------------------------ > > > > No need to miss a message. 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