[gmx-users] help for use the gromacs analysis tools

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 27 16:39:31 CET 2002

On Wed, 2002-11-27 at 16:11, bxiong wrote:
> Dear gromacs user:
> about six months ago, I use the ego program simulate a protein. recently, I want to use the gromacs analysis tools to analyze the result.  I use the pdb2gmx transform  the ego.pdb(charmm 19 polar H) to *.gro and *.top to produce the *.tpr. then use the gromacs analysis tools(such as g_gyrate) to do something. But the g_gyrate crashed and print a error message:
>      bus error (core dump)
> I think it may due to the hydrogen in the *ego.pdb (charmm polar H) did not match the *.gro(gromacs parameter). 
> can someone help me? thanks very much!!

you may have to reorder the pdb files from ego. You can do it with
trjconv if you provide a proper index file which you generate yourself.

>         bxiong
>         bxiong at mail.shcnc.ac.cn
>           2002-11-27
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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