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<p>The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that.</p>
<p>The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case.</p>
<p><br></p>
<p>Alex</p>
<p><br></p>
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<p><span class=rvts7>Dear Sir</span></p>
<p><br></p>
<p><span class=rvts7>I am using oplsaa force field. </span></p>
<p><span class=rvts7>In the .rtp file i did not found angles secion for any amino acid.</span></p>
<p><span class=rvts7>yes there are sections for dihedrals and impropers.</span></p>
<p><br></p>
<p><span class=rvts7>sorry for troubling you.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts8>Best</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts8>Anurag Dobhal</span></p>
<p><span class=rvts8>Juniour Research fellow</span></p>
<p><span class=rvts8>Supervisor: Dr. Ratnesh D. Jain</span></p>
<p><span class=rvts8>Department of chemical engineering</span></p>
<p><span class=rvts8>Insttute of Chemical Technology</span></p>
<p><span class=rvts8>400019, +91 8898486877</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>On Mon, May 4, 2015 at 1:03 PM, Alex <</span><a class=rvts9 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><br></p>
<p><span class=rvts7>"Which angles?" -- wait until Mark Abraham gets here.</span></p>
<p><br></p>
<p><span class=rvts7>You must have a very special version of aminoacids.rtp</span></p>
<p><br></p>
<p><span class=rvts7>Example: </span><a class=rvts9 href="https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp">https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp</a></p>
<p><br></p>
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<p><span class=rvts7>Thank you</span></p>
<p><br></p>
<p><span class=rvts7>But which angles I need to add in .rtp file.</span></p>
<p><br></p>
<p><span class=rvts7>are you talking about impropers and dihedrals ???</span></p>
<p><br></p>
<p><span class=rvts7>as In aminoacid.rtp there is no section for angles.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>Best</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>Anurag Dobhal</span></p>
<p><span class=rvts7>Juniour Research fellow</span></p>
<p><span class=rvts7>Supervisor: Dr. Ratnesh D. Jain</span></p>
<p><span class=rvts7>Department of chemical engineering</span></p>
<p><span class=rvts7>Insttute of Chemical Technology</span></p>
<p><span class=rvts7>400019, +91 8898486877</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>On Mon, May 4, 2015 at 12:47 PM, Sasha <</span><a class=rvts9 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><br></p>
<p><span class=rvts7>You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. </span></p>
<p><br></p>
<p><span class=rvts7>Alex</span></p>
<p><br></p>
<p><br></p>
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<p><span class=rvts7>Thank you for your reply.</span></p>
<p><br></p>
<p><span class=rvts7>I am simulating a PLGA (poly lactic co-glycolic acid molecle).</span></p>
<p><span class=rvts7>I get the topology file and I solvated the molecule. </span></p>
<p><span class=rvts7>my system is neutral.</span></p>
<p><span class=rvts7>while running the grompp I got 6 No default Ryckaert-Bell. types.</span></p>
<p><br></p>
<p><span class=rvts7>I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem.</span></p>
<p><br></p>
<p><span class=rvts7>I am using ions.mdp file which is given in the tutorial (lysozyme tutorial).</span></p>
<p><br></p>
<p><span class=rvts7>I have attatched the .pdb file and the .rtp parameters for them.</span></p>
<p><br></p>
<p><span class=rvts7>can you please check the parameters which I have given. so that I can rectify the errors.</span></p>
<p><br></p>
<p><span class=rvts7>awaiting for your reply.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>Best</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>Anurag Dobhal</span></p>
<p><span class=rvts7>Juniour Research fellow</span></p>
<p><span class=rvts7>Supervisor: Dr. Ratnesh D. Jain</span></p>
<p><span class=rvts7>Department of chemical engineering</span></p>
<p><span class=rvts7>Insttute of Chemical Technology</span></p>
<p><span class=rvts7>400019, +91 8898486877</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>On Mon, May 4, 2015 at 12:11 PM, Alex <</span><a class=rvts9 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><br></p>
<p><span class=rvts7>It may sound surprising, but this is resolved by either introducing</span></p>
<p><span class=rvts7>correct R-B term parameters in your topology/ff definitions, or by removing the mess from</span></p>
<p><span class=rvts7>the input coordinates, especially when non-bonded atoms are determined to</span></p>
<p><span class=rvts7>participate in a dihedral.</span></p>
<p><br></p>
<p><span class=rvts7>Humor aside, more information about the system is needed.</span></p>
<p><br></p>
<p><span class=rvts7>Alex</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>AD> Hello all</span></p>
<p><br></p>
<p><span class=rvts7>AD> How can I address the "No default Ryckaert-Bell. types error".</span></p>
<p><span class=rvts7>AD> The error is also in between the atoms which are not bonded with each other.</span></p>
<p><br></p>
<p><span class=rvts7>AD> Thank you</span></p>
<p><br></p>
<p><span class=rvts7>AD> --</span></p>
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<p><span class=rvts7>-- </span></p>
<p><span class=rvts7>Best regards,</span></p>
<p><span class=rvts7> Sasha </span><a class=rvts9 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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<p><span class=rvts7>-- </span></p>
<p><span class=rvts7>Best regards,</span></p>
<p><span class=rvts7> Alex </span><a class=rvts9 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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<p><span class=rvts11>-- </span></p>
<p><span class=rvts11>Best regards,</span></p>
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