Please kindly give me full information, even i have gone through few sites but I COULD NOT GET OUT OF MY errors.
You could do a web search for your ligand. Maybe someone else already developed OPLS-AA parameters for it and can provide a topology file (e.g. http://virtualchemistry.org).
Hi Satheesh,
I once did amylase-acarbose dynamics studies and I used GROMOS96 43A1.
I used PRODRG 2.5 (http://davapc1.bioch.dundee.ac.uk/prodrg/) to generate topology files for my ligand.
Hope this helps.
Cheers
You can use PRODRG server for creating the topology files for your ligand. Just copy and paste the coordinates from your pdb or mol file to the PRODRG server and it will give you a zip file in which itp and gro files are included. You can then include this gro file into the gro file of protein and then include the ligand itp file into the seq.top file.
Best Regards,
you can use ACPYPE server for prepare ligand topology. work with this server is simple. you can submit your molecule with mol2 format and then put net charge of your molecule then press submit.
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