subarna thakur wrote:
Hello,
I am running the pdb2gmx command for a homodimer protein with SF4 (a
ferro-sulphur cluster) ligand but it fails to generate the .gro file. A
error is coming SF4 not found in residue topology database. I have
trired all the different force fields. Can anybody please tell me how to
correct the error? How to modify the rtp file to consider the ligand?
Dealing with the error:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
The unfortunate news that you have your work cut out for you:
http://wiki.gromacs.org/index.php/Parameterization
http://wiki.gromacs.org/index.php/Exotic_Species
Parameterization is an advanced topic, especially when dealing with strange
species like an iron-sulfur cluster. Read the exotic species article closely.
-Justin
Subarna thakur
University of north bengal
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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