[gmx-users] re: help for gromacs tools

Rainer Boeckmann rboeckm at gwdg.de
Thu Nov 28 09:27:15 CET 2002

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...


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,
>        but you are doomed if you don't try.
>  Shanghai Institute of Materia Medica, Chinese Academy of sciences¡¡¡¡¡¡¡¡¡¡¡¡¡¡
>         Drug Discovery Design Center
> ¡¡      Bin Xiong
>         bxiong at mail.shcnc.ac.cn¡¡¡¡¡¡¡¡¡¡
> *****************************************************************
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2002-11-28
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

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


More information about the gromacs.org_gmx-users mailing list