[gmx-users] Residue 'UNK' not found in residue topology database

[SIMONE BROGI]

Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this messagge error:
"Residue 'UNK' not found in residue topology database"
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???
Thanks in advance for answers

Simone
--
Brogi Simone M.Sc. Ph.D.
Department of Pharmaceutical and Applied Chemistry
European Research Centre for Drug Discovery and Development
University of Siena
Via Aldo Moro
53100 Siena, Italy
Phone:[phone] e-mail: brogi32 at unisi.it simonebrogi1976 at hotmail.com
web: http://www.bronaldo.it http://www.natsyndrugs.org
blog: http://bronaldo.spaces.live.com/

[Justin Lemkul]

Post by SIMONE BROGI
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
"Residue 'UNK' not found in residue topology database"
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???

Most ligands are not part of existing force fields. Please consult the following:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

http://www.gromacs.org/Documentation/How-tos/Parameterization

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin
--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[naga sundar]

Dear simone

I think so u r using the same pr.mdp and md.mdp files
what u created initially. So open both the mdp files replace DRG with UNK
and the try sure it will work out.

Post by SIMONE BROGI
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
"Residue 'UNK' not found in residue topology database"
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???

http://www.gromacs.org/**Documentation/Errors#Residue_'**
XXX'_not_found_in_residue_**topology_database<http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database>
http://www.gromacs.org/**Documentation/How-tos/**Parameterization<http://www.gromacs.org/Documentation/How-tos/Parameterization>
http://www.gromacs.org/**Documentation/How-tos/Adding_**
a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
--
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[Justin Lemkul]

Post by naga sundar
Dear simone
I think so u r using the same pr.mdp and md.mdp files
what u created initially. So open both the mdp files replace DRG with UNK
and the try sure it will work out.

The error is from pdb2gmx, so .mdp alterations will have no effect. This error
is commonly encountered with a variety of generic residue names (UNK, LIG, DRG,
MOL, etc). pdb2gmx is not magic; it has limited support for any non-protein or
non-nucleic acid residues. Only a limited number of cofactors and molecules are
built into individual force fields, thus leaving the task of parameterization
and/or addition of species to a force field to the user.

-Justin

Post by naga sundar

Post by SIMONE BROGI
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
"Residue 'UNK' not found in residue topology database"
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???

http://www.gromacs.org/**Documentation/Errors#Residue_'**
XXX'_not_found_in_residue_**topology_database<http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database>
http://www.gromacs.org/**Documentation/How-tos/**Parameterization<http://www.gromacs.org/Documentation/How-tos/Parameterization>
http://www.gromacs.org/**Documentation/How-tos/Adding_**
a_Residue_to_a_Force_Field<http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field>
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
--
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* Please search the archive at http://www.gromacs.org/**
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--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================