On 6/12/12 3:30 PM, abhidon89 wrote:
an error occurred while running Grompp
Atomtype opls_977 not found
i have named atom type in the pdb file opls_977 for phosphorus .
The atom type should not appear in the .pdb file. If you have added some new
atom type to the OPLS force field, you need to add its parameters to
ffnonbonded.itp in order to actually make use of it.
Second
how can i make a rtp file ad how is it useful if forcefield residues are not
found.
Following this procedure:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
allows you to solve this error:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
in order to use pdb2gmx to generate the topology.
If you need further help, it would be best to state what you're trying to
accomplish and what exactly you have done thus far to try to address the problem
at hand.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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