[gmx-users] A question

[Mark Abraham]

samad ahadian wrote:
> Hello,
> 
> I am new user of Gromacs. I did a pdb2gmx command on my pdb file. I got an error below:
> 
> "Residue 'XXX' not found in residue topology database"
> 
> I know that I blindly made my pdb file using Materials Studio 4.2. Let me know there is a special software to make a pdb file? Thank you in advance for your response.

No, but you can certainly make life hard for yourself by using poor 
PDB-producing software, or using good software poorly. See 
http://wiki.gromacs.org/index.php/Errors for some background for this 
error. You need to generate a structure file whose residues and atoms 
are defined for the force field you intend to use, and which are named 
suitably so that pdb2gmx can recognize them. 'XXX' suggests that either 
MS4.2, or your usage of it, or both, are making life hard.

Depending on your level of newness, you should definitely do some 
background textbook/manual/literature reading, and/or tutorials.

Mark