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On 17/06/2011 12:33 AM, maria goranovic wrote:
<blockquote
cite="mid:BANLkTinvkNQE5+nGkyh_EEZ38Lv6hnWw4w@mail.gmail.com"
type="cite">thought of that, but the trajectory also has HISB data
.. </blockquote>
<br>
.xtc and .trr trajectories have no atom identification. That's why
lots of the tools require a .tpr or coordinate file, together with a
trajectory file in order to function. Using bash, look at gmxdump -f
traj.xtc 2>&1|less to learn what is there. You merely need to
be confident the atom ordering hasn't changed from whatever
generated the old trajectory.<br>
<br>
<blockquote
cite="mid:BANLkTinvkNQE5+nGkyh_EEZ38Lv6hnWw4w@mail.gmail.com"
type="cite">so I guess I will have to alter it frame by frame ? <br>
</blockquote>
<br>
Even if your trajectory is some pseudo-format like .pdb or .gro, you
can convert it back to one of the above easily.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTinvkNQE5+nGkyh_EEZ38Lv6hnWw4w@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Thu, Jun 16, 2011 at 4:32 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">On 16/06/2011 11:01 PM, maria goranovic
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi<br>
<br>
I had a simulation run with 4.0.7, using opls-aa for a
protein in water.<br>
<br>
I now use part of the protein coordinates output from
the simulation, and use pdb2gmx as:<br>
<br>
pdb2gmx -f conf.gro -ff oplsaa -ignh<br>
<br>
pdb2gmx complains that it cannot find HISB. I checked
that the topology files in 4.5.3 do not contain HISB,
while those in 4.0.7 do.<br>
<br>
It does not suffice to create another copy of the HISE
topology in the .rtp file and call it HISB, because a
number of hydrogen atoms also have been renamed?<br>
<br>
What can be done? I want to use 4.5.3 because I would
prefer to retain residue numbering<br>
</blockquote>
<br>
</div>
</div>
Rename all the HISB residues in your input coordinate file to
whatever OPLS/AA wants.<br>
<br>
Mark<br>
<font color="#888888">
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</font></blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</blockquote>
<br>
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