thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ? <br><br><div class="gmail_quote">On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5">On 16/06/2011 11:01 PM, maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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>