[gmx-users] Simulate the organic molecule => input / output error

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> Does the Gromacs only recognize the residues in the
> pdb file?

No... but pdb2gmx will only build a topology in an automated fashion if 
the residues are present in its databases.

> If they are not the standard amino acids in the library, Gromacs can't
> read, right???

A force field can potentially simulate species that are not present in 
the GROMACS .rtp database for that force field. See 
http://wiki.gromacs.org/index.php/Force_Fields and the links thereon.

You sound like you could benefit from some thorough reading of 
background material - like a textbook or the early chapters of the 
GROMACS manual. The donated time of users on this mailing list doesn't 
serve as a replacement for your time reading such reference material.

> Or, how does the Gromacs simulate the organic molecule?

Chapter 5 of the GROMACS manual has a partial example here.

> The command pdb2gmx could not produce the top and the gro file.
> Instead, it shows that   " File input/output error:   "

Well that means you made a file input/output error. You made another 
error in expecting us to guess what it was you did wrong. As I wrote 
here just yesterday to another user, you need to be much more specific 
to actually get useful help. See 
http://www.gromacs.org/pipermail/gmx-users/2008-May/034162.html

Mark