[gmx-users] How I can create a gromacs input file from a gamess output (one more question)

Marcelo de Freitas Lima mflima at qmc.ufsc.br
Tue Jul 13 14:59:56 CEST 2004

First, thanks Dr Dallas Warren and Ing. Vojtech Spiwok by your answers.

Other question now:

I want to create a pdf file from a organic dimer-molecule (about 	70 
atoms), not a biomolecule like a peptide or protein, only two 	identical 
molecules (each one with 35 atoms), to this I ran a ab 	initio 
calculation and now I have the z-matrix (in several formats, like mdl, 
xyz, etc.. except pdb format).

*****Imporant: I have no biological residues.***************

I tried to use PRODRG server to convert my dimer in a pdb file to 	 
perform a MD calculation with Gromacs, but the PRODRG server 		 
transforms my dimer in a monomer.

Ok, I tried run pdb2gmx with the monomer, but the message is:

"Fatal error: Residue 'UNK' not found in residue topology 			database"
This, because my molecule don't have aminoacids, or other biological 

My question:
I have to make my own .gro file by hand, or exist some tool to 		help in 

Thanks a lot!

Marcelo Lima

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