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

[Christopher Tran]

Quoting Marcelo de Freitas Lima <mflima at qmc.ufsc.br>:

> First, thanks Dr Dallas Warren and Ing. Vojtech Spiwok by your answers.
> 
> Other question now:
> 
> Explanation:
> ***********
> 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 
> residue.
> 
> My question:
> ***********
> I have to make my own .gro file by hand, or exist some tool to 
		help in 
> this?

editconf can convert pdb to gro for you.

> 
> Thanks a lot!
> 
> Marcelo Lima
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Christopher Tran
chr.tran at utoronto.ca