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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