Re: [AMBER] Ptraj image problems from Jayalakshmi Sridhar on 2010-05-13 (Amber Archive May 2010)

From: Jayalakshmi Sridhar <jsridhar.xula.edu>
Date: Thu, 13 May 2010 10:40:00 -0500

<div style="font-family: 'Times New Roman'; font-size: 1 6px;">Hi, I used this command t= o
 remove water in the pdb file that I obtained from the initial prmtop a= nd
 inpcrd files. grep -v 'WAT' 2a 6_init.pdb > 2a6_init_nowat.pdb I was then able to load 2a6_init_nowat.pdb and then the tr ajectory file that I obtained through ptraj imaging with nobox, nowate= r
 in vmd. It worked very well. I t= hank
 you all for taking time to get me through this problem. Jaya. On 05/12/10, Jason Swails <jason.swails.gmail.com> wrote:<b lockquotecite="mid:AANLkTilFLH2NLgxF5sRivYJNQbO3q0U8wl71pnOFMknU. mail.gmail.com" class="iwcQuote" style="border-left: 1= px
 solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0p t;" type="cite"><div class="mimepart text plain">H ello, Don't forget that you are stripping the wat er. If you haven't already, you have to remake the top ology file without the water residues present, or you will ge= t
 the effect you're seeing (I'm assuming this is what's happening) . You can load your prmtop file into rdparm, use the command stripwater, and save the new prmtop to use with V MD, but it's too old to be used for calculations in my expe rience. (And you can't use Amber 7 parm, you have to use the other parm in VMD) Another alternative is to use one of the PDB files you created and run it through leap to get the prmtop (this would probably be easier if you don't have = any
 custom ligand and/or custom residues). Hope thi= s
 helps, Jason On Wed, May 12, 2010 at 4:23 PM, Jayalakshmi Sridhar <jsridhar.xula.edu>w rote: > My earlier mail got marked up. So, I am resending it. > I ran the script for 5 frames wi= th
 trajout to pdb files as suggested. I got > 5 pdb fi les. Each of them loaded normally in vmd without any streaks. The<= br
 />> avg structure in the earlier run and in the present 5 fr= ame
 run looked > normal in vmd. > Jaya . > > On 05/12/10, Thomas Cheatham I II <tec3.utah.edu> wrote: > &gt ; > > > > > After putting the trajout statement after the strip command, I do not > > > see the box shape. The number of frames are also consistent with 2400 > > > frame s. But the atoms are still streaking in the vmd display. I am > > > attaching a picture of the image as jpg fi le. Jaya. > > > > The position of the trajout, in all versions of ptraj, is irrelevant. > > What is likely true is that there is a mismatch between your trajectory > > and your loaded prmt= op
 (as mentioned by Prof. Simmerling). (By the > > way, from the scripts shown previously you loaded AMBER traje ctory format > > files, not binpos). > > > > The offsets seen in your mo vie are consistent with the AMBER trajectory > > not having box information, but the prmtop having box information (or > > vise-versa). In this case, usually the f irst frame (in a VMD movie) > looks > & gt; OK, and subsequent ones get shifted. > > > > To verify things are OK and its a prmtop mis match, do your script the > same > & gt; for ~5 frames... > > &gt ; > trajin mdcrd 1 5 1 > > &g t; > and change the trajout to PDB files and look at these. > > > > trajout tmp-pdb pdb > > > > (or also look at you= r
 avg.pdb) > > > > --tec 3 > > > > > >_____________________ ________________________ __ > > AMBER mailing list > & gt; AMBER.ambermd.org > > <a href="ht tp://lists.ambermd.org/mailman/listinfo/amber"target="_bl ank">http://lists.ambermd.org/mailman/listinfo/amber</a>( > <a href="http://lists.ambermd.org/mailman /listinfo/amber%29"target="_blank">http://lists.amber md.org/mailman/listinfo/amber)</a> > > > > > > __ ________________________ _____________________ > AMBER mailing list > AMBER.ambermd.org > <a href="http://lists.ambermd.org/mailman/list info/amber"target="_blank">http://lists.ambermd.org/m ailman/listinfo/amber</a> > > -- Jason M. Swails Quantum T heory Project, University of Florida Ph.D. Gradu ate Student 352-392-4032 __________ ________________________ _____________ AMBER mailing list AMBER.ambermd.org <a href="http://lists.ambe rmd.org/mailman/listinfo/amber"target="_blank">http://l ists.ambermd.org/mailman/listinfo/amber</a> </div>< /blockquote></div>

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Received on Thu May 13 2010 - 09:00:03 PDT