<p>Hi Jernej,</p>
<p>You can copy the charmm27.ff directory to your working directory and make changes locally.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Dec 14, 2011 2:54 AM, "Jernej Zidar" <<a href="mailto:jernej.zidar@gmail.com">jernej.zidar@gmail.com</a>> wrote:<br><br>Hi Mark.<br>
>> How will pdb2gmx "know" it has to parse the monomeres.rtp file?<br>
>It can't. You must add to an existing .rtp file.<br>
<br>
That's a problem (and a negative surprise), because I can't just add a<br>
new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and<br>
CGenFF are two different things, though they can be used together.<br>
<br>
>I will add that you will also have to add the residue to aminoacids.dat<br>
>file, so that the polymer repeat unit is recognized. for your small<br>
>polymer molecule you can just generate from the swissparam website<br>
<br>
That could well work in the case of the smallest polymer that is<br>
composed of just five monomers, but it is absolutely out of the<br>
question in the case of experimentally-relevant polymers that are<br>
composed of at least 40 units.<br>
<font color="#888888"><br>
Jernej<br>
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