[gmx-users] Dipeptide generation problem [Justin]

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 26 18:22:14 CEST 2010

----- Original Message -----
From: Eudes Fileti <fileti at ufabc.edu.br>
Date: Friday, August 27, 2010 2:15
Subject: Re: [gmx-users] Dipeptide generation problem [Justin]
To: gmx-users at gromacs.org

> Olá Justin, > thank you for responding to my post. I had tried what you mentioned before. > All I get is that the some atoms are missing (see error message in the > link https://sites.google.com/site/fileti/ ). > In fact, as I just want NH3+ (from LYS) and COO- (from ASP), the other atoms are not included > in PDB file and this can give error. If I put everything into the same group ("1" for example) many  > of the atoms are deleted by pdb2gmx because they are duplicates.> 
> In fact I still do not quite understand the logic of creating a PDB from the aminoacid residues. > I've read some tips on the list but still I could not understand.

Have a look some MD tutorial material (doesn't have to be GROMACS). They probably start with a well-formed PDB file. That's probably a better learning experience than trying to read the format description.

Alternatively, use a molecule builder (search webpage for suggestions here) to create the coordinates, and then get pdb2gmx to do the rest of the work.

The idea behind pdb2gmx is that you don't have to move mountains to get your termini right, and the corresponding topology. If you just give it two adjacent PHE (charged or not), you can tell pdb2gmx what termini you want it to have. Done right, this whole task should not require you to inspect or change a coordinate file at all.


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