Liu Shiyong wrote:
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
This is one of the more explicit and helpful error messages. It tells you why
you can't do what you want and also tells you exactly how to fix it. Doing
fitting and PBC correction in one trjconv command may have "worked" in a
previous version, but it's never been correct to do so.
-Justin
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
-------------------------------------------------------------------
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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