Dear Colleagues, I want to extract PDB snapshot from trajectory file by following command. It works in 4.0, but not in 4.5
pdb=1akk trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc -dt 20 -b 0 -o ${pdb}_gromos53a6_MD2.traj.nojump.pdb -fit rot+trans -pbc nojump Program trjconv, VERSION 4.5.3 Source code file: gmx_trjconv.c, line: 854 Fatal error: PBC condition treatment does not work together with rotational fit. Please do the PBC condition treatment first and then run trjconv in a second step for the rotational fit. First doing the rotational fit and then doing the PBC treatment gives incorrect results! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best Shiyong -- Shiyong Liu ------------------------------------------------------------------ Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel:86-27-87558335-805 ------------------------------------------------------------------ Chinese Version: ------------------------------------------------------------------ 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编:430074 电话:86-27-87558335-805 -------------------------------------------------------------------
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