Dear gromacs users,<div>I think I solved the problem.</div><div>I converted armonic angle potentials in the
Urey-Bradley potentials using 0 as constant for the</div><div>1-3 bond potential.</div><div><br></div><div>Is it right in your opinion?</div><div><br></div><div>Francesco</div><div><br><div class="gmail_quote">2012/5/16 francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear gromacs users,<div><br><div>I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force field.</div><div>
<br></div><div>I downloaded the charmm files toppar_carb_apr12.tgz from <a href="http://mackerell.umaryland.edu/CHARMM_ff_params.html" target="_blank">http://mackerell.umaryland.edu/CHARMM_ff_params.html</a></div>
<div>and I converted bonded and nonbonded parameters in gromacs format through the script <a href="http://convert_charmm_to_gromacs.pl" target="_blank">convert_charmm_to_gromacs.pl</a>.</div><div><br></div><div>I have successfully generated the .top, using pdb2gmx, as well. </div>
<div><br></div><div>But when I run grompp, it complains with errors like:</div><div><br></div><div><b>No default Angle types </b></div><div><b><br></b></div><div>and</div><div><br></div><div><b>No default Improper Dih. types</b></div>
<div><div><br></div><div><br></div><div>Look at the attacched file for the complete output from grompp.</div><div><br></div><div><br></div><div>Now I inspected the missed interaction and, at least for the angle part, I figured out the problem.</div>
<div>In the original charm parametrization there are angles parametrized as armonic and other angles</div><div>parametrized as Urey-Bradley. Moreover, as far as I know, in the rtp file only one form can be used</div><div>
because of the [ bondedtypes ] clause.</div><div><br></div><div>So my question is: Is there any way to mix, in the same residue (and hopefully in the same .rtp file), </div><div>angles parametrized in the armonic form and Urey-Bradley parametrized angles? </div>
<div><br></div><div>Is a correct solution parametrizing everything as armonic angles and mimic the bond potential between</div><div>atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value?</div><span class="HOEnZb"><font color="#888888"><div>
<br></div><div><br></div>Francesco<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
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