Bhawana Gupta wrote:
Hello sir,
From last few days , i was using TINKER for implicit simulations using
force field oplsaa
Now for explicit one, i switched to gromacs version 4.0.But if i take
pdb file from tinker (molecular modelling software) and paste it in The
Dundee Prodrg server. i got my *.itp file, *.gro file.
This server generates a topology that is possibly suitable for use with
one specific force field.
But if i use force field as ffoplsaa or ffG43a1 or any other force field
except ffgmx. I always got error in atom type not found.
As expected.
Tell me what to do.
Can i switch to gromacs older version i.e.3.3.1???
No.
Whether i can use The Dundee Prodrg server for peptides having usual
amino acid???
You can, but pdb2gmx will give a wider choice of force field with more
reliable parameters - for the usual residues.
Mark
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