<div style="font-family: 'Times New Roman'; font-size: 1 6px;"><br />I ran the script for 5 frames with trajout to pdb files as suggested. I got 5 pdb files. Each of them loaded normally = in
vmd without any streaks. The avg structure in the earlier run and i= n the
present 5 frame run looked normal in vmd.<br _moz_dirty== ""
/>Jaya.<br _moz_dirty="" /><br /><span>= On
05/12/10, <b class="name">Thomas Cheatham III </b> & lt;tec3.utah.edu>wrote:</span><blockquotecite=" mid:Pine.WNT.4.64.1005121359170.5316.guanine"class=" iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); pa dding-left: 13px; margin-left: 0pt;" type="cite"><di= v
class="mimepart text plain"><br />> After putting t= he
trajout statement after the strip command, I do not <br />>= ;
see the box shape. The number of frames are also consistent with 2= 400
<br />> frames. But the atoms are still streaking in th= e vmd
display. I am <br />> attaching a picture of the imag= e as jpg
file. Jaya.<br /><br />The position of the trajout,= in all
versions of ptraj, is irrelevant. <br />What is likel= y true is
that there is a mismatch between your trajectory <br />and= your loaded
prmtop (as mentioned by Prof. Simmerling). (By the <= br />way,
from the scripts shown previously you loaded AMBER traject= ory format <br
/>files, not binpos).<br /><br />The offs= ets seen in your
movie are consistent with the AMBER trajectory <br />= not having box
information, but the prmtop having box information (or = <br
/>vise-versa). In this case, usually the first frame (in = a VMD
movie) looks <br />OK, and subsequent ones get shifted.<= br
/><br />To verify things are OK and its a prmtop mismatch, do= your
script the same <br />for ~5 frames...<br /><br />trajin mdcrd 1 5 1<br /><br />and change the trajout to PDB files and look at these.<br /><br />trajout tmp-pdb pdb<br / ><br />(or also look at your avg.pdb)<br /><br />--tec3< br /><br /><br />_______________ ________________________ ________<br />AMBER mailing list<br />AMBER.am bermd.org<br /><a href="
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http://lists.ambermd. org/mailman/listinfo/amber</a><br/></div></blockquote>< /div>
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Received on Wed May 12 2010 - 13:30:08 PDT
