<html><head></head><body>just have charmm27.ff/forcefield.itp #include your new files. If you want pdb2gmx to work, you will need to create the appropriate .rtp and/or .hdb files too<br>
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Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="gmail_quote">Fabian Casteblanco <fabian.casteblanco@gmail.com> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<pre style="white-space: pre-wrap; word-wrap:break-word; font-family: monospace">Hello all,<br /><br />I'm building a drug molecule using CHARMM parameters. The thing is<br />that there is this new CGenFF (an extension of CHARMM, but very<br />similar to the old CHARMM atom types<br /><a href="http://mackerell.umaryland.edu/~kenno/cgenff">http://mackerell.umaryland.edu/~kenno/cgenff</a>/) that uses better<br />parameters for drug-like molecules. I would like to use these new<br />parameters for this drug molecule (pretty big molecule). I took all<br />the parameter values from CGenFF and I converted them to values used<br />by Gromacs and I formatted it just like the original ffcharm27.itp<br />files found in Gromacs. The only thing is that when it comes to<br />Lennard Jones,1-4 parameters, CHARMM gives you the actual individual<br />value by atom whereas Gromacs has already all the pair listed values<br />stored. Is there any way that I can place these 1-4 parameters i
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the<br />drug.itp file itself and have Gromacs calculate the combinations just<br />as it does for the regular LJ values?<br /><br />I have:<br />-CgenFFbon.itp (bonded, angle, dihedral parameters,etc)<br />-CgenFFnb.itp (nonbonded LJ values)<br />-CgenFF.atp (atom type file)<br /><br />What exactly do I need to include on my drug.itp (or drug.top) file<br />inorder so it can read these parameters from the files above?<br /><br />Thanks for anyones help! Greatly appreciated!!<br /><br />;SAMPLE topology:<br />;<br />;<br />; Include forcefield parameters<br />#include "charmm27.ff/forcefield.itp"<br /><br />#include "drug.itp"<br /><br />[ system ]<br />; Name<br />DrugName<br /><br />[ molecules ]<br />; Compound #mols<br />DDD 1<br /><br />-- <br />Best regards,<br /><br />Fabian F. Casteblanco<br />Rutgers University --<br />Chemical Engineering PhD Student<br />C: +908 917 0723<br />E: fabian.casteblanco@gmail.com<br />-- <br />gm
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