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
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