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

Ing. Vojtech Spiwok Vojtech.Spiwok at vscht.cz
Wed Jul 14 08:39:04 CEST 2004

>Date: Tue, 13 Jul 2004 09:59:56 -0300
>From: Marcelo de Freitas Lima <mflima at qmc.ufsc.br>
>Subject: [gmx-users] How I can create a gromacs input file from a
>gamess output (one more question)
>To: gmx-users at gromacs.org
>Message-ID: <40F3DCCC.2020508 at qmc.ufsc.br>
>Content-Type: text/plain; charset=us-ascii; format=flowed
>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.

You can do this for each monomer and combine them, just turn
minimization option of PRODRG off. If you want to use distances
from ab initio minimization (was it minimization ?) you have to edit
topology file and change bond lenght parameters, otherwise you
get default bond lenghts after the first minimization in gromacs.

>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 

You have to add a line saying that you include itp file in top file.
Follow prodrg tutorial :

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

PRODRG will do this. Follow the tutorial.

>Thanks a lot!
>Marcelo Lima

You are welcome
Vojtech Spiwok

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