[gmx-users] Protein with ligand

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Mon Apr 21 11:29:00 CEST 2003

Hi Rahul,

I suggest you have a look at this web page:


You´ll find there an excellent tutorial!
Hope this help,
with best regards,

Rahul Banerjee wrote:

> Dear All,
>         I was trying to simulate a protein with a
> ligand. But it was giving Fatal error because the
> topology of the was not known to pdb2gmx. Now I
> created topology for that molecule using PRODRG
> server. I am not getting where I have to add the
> topology(and with what extension) so that I can
> proceed.
>         Thanking you in anticipation,
> With best wishes,
> Rahul Banerjee
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Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144,  28006  MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18

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