Parthiban Marimuthu wrote:
Hi
can any one help me in sorting out the file conversion error,
when using PRODRG server for converting pdb - gromacs topology format
for small molecule.
the error message displayed in gromacs was
Atomtype CH3 not found (while using amber99 FF)
or
Atomtype CH1 not found (while using GMX)
or
Atomtype NR not found (while using G43a1)
the small molecule was derived from pubchem and conformation was
converted using Maestro with proper charges and EM.
PRODRG is designed for use with ffgmx, which is outdated and should not be used.
PRODRG beta produces topologies compatible with 43A1. Your errors indicate
you're mixing and matching force fields, which, even if it worked, would produce
nonsense output.
-Justin
Thanks
Parthiban.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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