Sorry, but first I suggest: Read the error message!
Fatal error:
> Residue 'UNK' not found in residue topology database
Now, what could this mean? This actually means, in the forcefield
residue database (e.g. ffoplsaa.rtp) exists no entry for a molecule
named UNK...
Rename the pdb to the expected name given in the rtp of the forcefield
for your molecule, or if, more likely, the molecule really doesn't exist
you have to build an entry by either building it from reasonable
available building blocks or parameterize it yourself...
And in general there's a very important rule to obey before posting to
this mailinglist: RTFM...
bye
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Sagittarius wrote:
Dear Gromacs users,
Could you please help me to find out what the problem is.
I use command
pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p
outputName.top
formaldehyde.pdb looks like this:
COMPND UNNAMED
REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers
REMARK 1 pertain to the .dat file from which this file was created,
REMARK 1 not to one created from this file:
REMARK 1 PDB: 1 2 3 4
REMARK 1 MMOD: 1 2 3 4 /
HETATM 1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0
HETATM 2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0
HETATM 3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0
HETATM 4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0
CONECT 1 3 4
CONECT 1 2
CONECT 1 2
CONECT 2 1
CONECT 2 1
CONECT 3 1
CONECT 4 1
END
Gromacs output is
-------------------------------------------------------
Program pdb2gmx, VERSION
Source code file: C:\Program Files\Microsoft Visual
Studio\MyProjects\pdb2gmx\pdb2gmx\resall.cpp, line: 493
Fatal error:
Residue 'UNK' not found in residue topology database
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Thank you in advance
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