[gmx-users] how to add topology for a new residue

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Fri Apr 25 11:25:01 CEST 2003

Dear Sridhar,

Have a little look to this web page:


You´ll find there an excellent tutorial made by Dr. Kerrigan
Hope this help,
with best wishes,

"Mr.Sridhar" wrote:

> I have a problem in running MD of a protein which has
> PHORBOL-13-ACETATE as a bound ligand. I got a gromacs topology file from
> PRODRG server. But I don't know how to include this topology file in Gromacs
> and run MD.
> I've added the line #include "PRB.itp"
> in the main gromacs forcefield file "ffgmx.itp" but it is not working.
> I'll be happy if anybody can find the procedure for this.
> Thanks.
> sridhar.
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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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