<br><br><div class="gmail_quote">On Thu, Aug 18, 2011 at 3:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Roland Schulz wrote:<br>
> Hi,<br>
><br>
> you can use trjconv for that (or editconf). You probably would want to<br>
> add some waters though.<br>
><br>
<br>
</div>For trjconv, you can get a coordinate file, but not a .cpt; editconf throws a<br>
fatal error (unless I'm using it wrong, but I tried -f state.cpt). If you try<br>
to output a .cpt from trjconv, it gives you file.cpt.xtc. Is there some other<br>
way to preserve a state that's not given in the documentation? You can write a<br>
.trr file, but that only gives you velocities.<br></blockquote><div><br></div><div>Yes, one can only get coordinates and velocities. But as you said, it doesn't make sense to get the full state.</div><div><br></div><div>
Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<div class="im"><br>
> Roland<br>
><br>
> On Thu, Aug 18, 2011 at 2:50 PM, Peter C. Lai <<a href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>
</div><div class="im">> <mailto:<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>>> wrote:<br>
><br>
> Is there anyway I can extract a subset of atoms from a cpt file,<br>
> like I can<br>
> with trjconv operating on a traj file? I want to remove a ligand and<br>
> still<br>
> keep all the remainder of the state information, so I can feed this back<br>
> into grompp with a modified topology and "continue" a run without<br>
> the ligand.<br>
><br>
> --<br>
> ==================================================================<br>
> Peter C. Lai | University of Alabama-Birmingham<br>
> Programmer/Analyst | BEC 257<br>
> Genetics, Div. of Research | 1150 10th Avenue South<br>
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</div><div class="im">--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>