<div dir="ltr">Hi, I have tried to create prm and psf file from a gromacs tpr file with tpr2psf.py , from the link <a href="https://github.com/pmamonov/tpr2psf">https://github.com/pmamonov/tpr2psf </a> and I encounter the error FF parameters Bonds: 93 Angles: 38 Proper dihedrals: 176 Ryckaert-Belleman dihedrals: 0 Improper dihedrals: 25 Traceback (most recent call last): File "tpr2psf.py", line 400, in <module> tpr.print_ff(prm) File "tpr2psf.py", line 342, in print_ff print >>f, "%.5f 0 %.4f" % (imp.k*j2cal/2, imp.psi) AttributeError: STUFF instance has no attribute 'psi' can anyone tell me how to overcome ? thank you <a href="https://github.com/pmamonov/tpr2psf"></a> On Saturday, August 28, 2010 5:21:54 PM UTC+5:30, Peter wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Dear All, Some time ago I wrote a (python) code to convert GROMACS binary TPR files into CP2K readable PSF (topology) and PRM (FF parameters) files. Unfortunately I didn't achieve exact match between energies calculated by GROMACS and CP2K/FIST. Respective energies calculated by GROMACS and CP2K/FIST match in case of bonds, angles and sometimes dihedrals. Nonbonded interactions (Coulomb and VdW, both long range and 1-4) are different for most of tested systems. Gradients calculated by both codes for some large system correlate with covariance coefficient 0.4. At some point I considered this result satisfactory and moved on. For now I don't have an intention to further improve this conversion tool, but probably others will find it to be a good starting point for creating such a conversion tool or probably try it as-is. So I put an archive with script, auxillary library (modified libgmx wrapper by Martin Hofling [<a href="http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003183.html" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Foldwww.gromacs.org%2Fpipermail%2Fgmx-developers%2F2009-March%2F003183.html\46sa\75D\46sntz\0751\46usg\75AFQjCNHmVM2yFP9PmTgAdUykq24dlWOLew';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Foldwww.gromacs.org%2Fpipermail%2Fgmx-developers%2F2009-March%2F003183.html\46sa\75D\46sntz\0751\46usg\75AFQjCNHmVM2yFP9PmTgAdUykq24dlWOLew';return true;">http://oldwww.gromacs.org/pipermail/gmx-developers/ 2009-March/003183.html</a>]) and some sample files here: <a href="http://groups.google.com/group/cp2k/web/gmx2psf.tar.bz2" target="_blank" onmousedown="this.href='http://groups.google.com/group/cp2k/web/gmx2psf.tar.bz2';return true;" onclick="this.href='http://groups.google.com/group/cp2k/web/gmx2psf.tar.bz2';return true;">http://groups.google.com/group/cp2k/web/gmx2psf.tar.bz2</a> Best regards, Peter Mamonov Lomonosov Moscow State University Biological faculty biophysics dept. P.S. Here is a help message from script, which provides some additional info: ABOUT: This script reads GROMACS .tpr file and produces .psf and .prm files readable by CP2K[ <a href="http://cp2k.berlios.de/" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fcp2k.berlios.de%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNG8a04cBV6g-qX2gL0GLMujwBbc_g';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fcp2k.berlios.de%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNG8a04cBV6g-qX2gL0GLMujwBbc_g';return true;">http://cp2k.berlios.de/</a>] and probably some other MM software. This script uses modified version of GROMACS library python wrapper, written by Martin Hofling [<a href="http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003183.html" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Foldwww.gromacs.org%2Fpipermail%2Fgmx-developers%2F2009-March%2F003183.html\46sa\75D\46sntz\0751\46usg\75AFQjCNHmVM2yFP9PmTgAdUykq24dlWOLew';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Foldwww.gromacs.org%2Fpipermail%2Fgmx-developers%2F2009-March%2F003183.html\46sa\75D\46sntz\0751\46usg\75AFQjCNHmVM2yFP9PmTgAdUykq24dlWOLew';return true;">http://oldwww.gromacs.org/pipermail/gmx- developers/2009-March/003183.html</a>]. NB: This script IS NOT capable of exact conversion between tpr and psf/ prm topology/force field representation. Respective energies calculated by GROMACS and CP2K/FIST match in case of bonds, angles and sometimes dihedrals. Nonbonded interactions (Coulomb and VdW, both long range and 1-4) are different for most of tested systems. Gradients calculated by both codes for some large system correlate with covariance coefficient 0.4. REQUIREMENTS: * GROMACS dynamic libraries (libgmx*.so) * Modified version of GromPy wrapper (distributed with this script) USAGE: tpr2psf.py system.tpr Will produce system.psf and system.prm </blockquote></div>