[gmx-users] re: help for gromacs tools

[Rainer Boeckmann]

Hi Bin Xiong,

...the tpr-file is only necessary if you need forcefield-information for your analysis. Thus you would need one for calculating electrostatic potentials but a pdb-file would be enough for rms-analysis.
But be careful with the hydrogen-ordering/-naming! In the end you will find it useful to spend some time on constructing a proper tpr-file...

Cheers,
rainer

bxiong wrote:

> Dear    David & all:
> thanks, David. I write a small program to cat the all *.ego.pdb file to the one *.pdb , each has a MODEL 1(2,...) begin with the ATOM and end with ENDMDL. but I don't know how the gromacs tools work?
> 1,  is the tpr  necessary?  and I find the *.tpr can use other file format (such as pdb ....). If It can use the pdb format,  I think the question become easy.
> 2,  and if I provide a correct *.idx file. It can work well?
> thank you !!
>
>
>
> Best regards for you!
>
> ****************************************************************
>        You may be disappointed if you fail,
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>  Shanghai Institute of Materia Medica, Chinese Academy of sciences¡¡¡¡¡¡¡¡¡¡¡¡¡¡
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> ¡¡      Bin Xiong
>         bxiong at mail.shcnc.ac.cn¡¡¡¡¡¡¡¡¡¡
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--
Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

Tel.: +49(551)201-1141, Fax.: +49(551)201-1089
email: rboeckm at gwdg.de

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