<font size="4">check your aminoacid.rtp file present in <br>/usr/share/gromacs/top/oplsaa.ff/<br>check all the atom types of that particular residue in your pdb file and match them properly with the atoms types present in the aminoacid.rtp file .....and then proceed ....</font><br>
<br><div class="gmail_quote">On Tue, Jun 12, 2012 at 5:29 PM, delara aghaie <span dir="ltr"><<a href="mailto:d_aghaie@yahoo.com" target="_blank">d_aghaie@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-size:12pt;font-family:arial,helvetica,sans-serif"><div>Dear Gromacs users</div><div>Using bdp2gmx command to obtain topology and .gro file for 1AU1.pdb I get the following error:</div><div>I should mention that I have selected OPLS force field.</div>
<div><br></div><div>1) how can I reach to the conclusion that special forcefield is better fo my system?</div><div><br></div><div>2) This is the error:</div><div><br></div><div>-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.5<br>Source code file: pdb2gmx.c, line: 655<br><br>Fatal error:<br>Atom HB3 in residue ARG 71 was not found in rtp entry ARG with 24 atoms<br>while sorting atoms.<br><br>For a hydrogen, this can be a different protonation state, or it<br>
might have had a different number in the PDB file and was rebuilt<br>(it might for instance have been H3, and we only expected H1 & H2).<br>Note
that hydrogens might have been added to the entry for the N-terminus.<br>Remove this hydrogen or choose a different protonation state to solve it.<br>Option -ignh will ignore all hydrogens in the input.<br>For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------</div><div>Any help would be greatly appreciated..</div>
<div>Thanks</div><div>Regards</div><div>D.M<br></div><div><br></div><div><br></div><div><br></div></div></div><br>--<br>
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Molecular Simulation Lab.<br>Chemistry and Physics of Materials Unit<br>Jawaharlal Nehru Centre for Advanced Scientific Research <br>Jakkur P. O. <br>Bangalore - 560 064<br>Karnataka, INDIA<br>Ph. (lab) : +91-80-22082809 </b></i></font><br>