PAVAN PAYGHAN wrote:
HI
i have generated a topology file for drug using prodrg with gromos
96.1force field , now i want to use it for simulation with DNA in
complex. I am using amber 03 force field for my system . i have included
correctly the drg.itp file in generated topology file for DNA alone
(using pdb2gmx).
i managed to run upto genbox successfully ,but when i tried to run
grompp it showed error
"Atom type 'CH1' not found !"
where i have to modify the things to work it properly .
Start by not mixing force fields. There is no reason to believe that anything
produced by PRODRG would be compatible with an AMBER force field. Hence why
PRODRG says it produces GROMOS-compatible topologies, with no mention of AMBER
of any of the others. The underlying derivation of the force fields and general
theory (united-atom vs. all-atom being a major one) make these force fields
incompatible.
To properly treat your system, it should be fairly straightforward to use
antechamber or acpypi to develop your ligand parameters.
-Justin
--
========================================
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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