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
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