[gmx-users] trjconv with superposition

[Justin A. Lemkul]

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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