Hello,
I need to perform some MD calculations and then trajectories of some
small molecules analyzed.
What I have is
1. protein
2. cofactor (FAD)
3. small molecule (either single O2 atom or single Chlorine atom)
4. crystallographic waters
The software I can access is either Gromacs (with yum install) or
perhaps Desmond.
I have tried and tried to get this to run (for 6 months perhaps), to no
avail. The input files located on the web do not work on the version of
Gromacs provided by the yum install command. The Maestro license
(required in order to get Desmond to run) is too expensive.
Is there a kind soul somewhere that would have suitable input files that
would do all the above steps and who'd be willing to pass them on to me?
What needs to be done is:
add waters to the crystallographic waters in order to fill a box of
suitable size
generate parameter and topology files for each component separately
merge these into global parameter and topology files for the system
run initial Energy Minimization
run M.D. simulations
analize the trajectories of the small molecules.
Thanks in advance.
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
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